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This page was generated on 2024-05-04 11:38:54 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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    TIMEOUT  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for biodbChebi on lconway


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: 2024-05-03 20:25:23 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 20:29:23 -0400 (Fri, 03 May 2024)
EllapsedTime: 240.2 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 beta (2024-04-14 r86421)
* using platform: x86_64-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 Monterey 12.7.1
* 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-x86_64/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 beta (2024-04-14 r86421) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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 [2024-05-03 20:26:24.574][biodb::testContext]
biodb.INFO [2024-05-03 20:26:24.579][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:26:24.581][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-05-03 20:26:24.583][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:26:24.584][biodb::testContext]
biodb.INFO [2024-05-03 20:26:24.593][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:26:24.596][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 20:26:24.607][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:26:24.608][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 20:26:24.610][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 20:26:24.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.616][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 20:26:24.645][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 20:26:24.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.649][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 20:26:24.651][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 20:26:24.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.655][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 20:26:24.656][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 20:26:24.658][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 20:26:24.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.664][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 20:26:24.665][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 20:26:24.666][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 20:26:24.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.687][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 20:26:24.689][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 20:26:24.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.694][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 20:26:24.695][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 20:26:24.696][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 20:26:24.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.700][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 20:26:24.701][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 20:26:24.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.705][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 20:26:24.706][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 20:26:24.707][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 20:26:24.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.712][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:26:24.713][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 20:26:24.715][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 20:26:24.716][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 20:26:24.717][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 20:26:24.718][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 20:26:24.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.723][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 20:26:24.724][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 20:26:24.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.729][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 20:26:24.730][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 20:26:24.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.735][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 20:26:24.736][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 20:26:24.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.741][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 20:26:24.742][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 20:26:24.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.748][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 20:26:24.749][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 20:26:24.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:24.754][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:26:24.756][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 20:26:24.985][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 20:26:24.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.990][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[2024-05-03 20:26:24.991][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 20:26:24.993][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 20:26:24.994][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 20:26:24.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:24.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:24.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.001][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 20:26:25.050][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.074][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-03 20:26:25.076][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.077][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:26:25.079][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.080][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.082][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.083][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.085][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:26:25.086][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:26:25.087][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.089][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 20:26:25.091][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:26:25.092][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.093][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.095][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:26:25.095][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:26:25.095][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:26:25.095][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:26:25.095][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:26:25.096][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:26:25.098][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.099][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.101][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:26:25.102][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.103][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.104][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.106][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.107][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:26:25.109][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:26:25.110][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.111][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.113][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 20:26:25.116][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.117][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:26:25.118][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.119][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:26:25.121][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.122][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.123][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.125][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.126][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:26:25.127][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:26:25.128][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.130][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 20:26:25.131][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:26:25.132][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.133][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.135][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:26:25.135][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:26:25.135][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:26:25.135][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:26:25.135][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:26:25.136][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:26:25.138][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.139][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.140][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:26:25.142][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.143][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.144][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.146][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.147][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:26:25.148][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:26:25.149][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.151][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.152][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 20:26:25.155][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.156][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-03 20:26:25.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.159][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:26:25.161][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.162][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.163][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.165][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.166][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:26:25.167][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:26:25.169][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.171][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 20:26:25.172][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:26:25.173][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.175][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.176][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.178][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:26:25.179][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.190][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:26:25.192][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.193][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.194][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.196][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.197][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:26:25.199][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:26:25.200][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.201][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.203][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 20:26:25.205][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.207][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:26:25.208][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.210][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:26:25.211][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.212][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.214][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.215][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.217][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:26:25.218][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:26:25.219][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.221][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 20:26:25.222][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:26:25.223][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.224][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.226][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.227][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:26:25.228][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.229][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.231][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:26:25.232][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.234][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.236][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.237][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:26:25.238][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:26:25.240][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.241][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:26:25.247][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:26:25.249][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.250][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[2024-05-03 20:26:25.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.257][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[2024-05-03 20:26:25.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.319][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[2024-05-03 20:26:25.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.344][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.DEBUG[2024-05-03 20:26:25.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.358][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 20:26:25.365][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 20:26:25.367][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 20:26:25.369][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 20:26:25.372][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:26:25.374][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 20:26:25.376][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 20:26:25.378][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 20:26:25.381][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 20:26:25.382][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 20:26:25.384][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:26:25.387][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 20:26:25.389][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 20:26:25.391][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 20:26:25.393][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 20:26:25.395][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:26:25.397][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 20:26:25.399][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 20:26:25.401][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:26:25.403][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 20:26:25.404][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 20:26:25.406][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 20:26:25.408][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 20:26:25.410][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 20:26:25.412][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 20:26:25.414][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 20:26:25.416][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 20:26:25.418][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 20:26:25.420][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 20:26:25.422][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 20:26:25.424][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 20:26:25.426][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 20:26:25.427][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 20:26:25.429][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 20:26:25.431][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 20:26:25.433][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 20:26:25.435][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 20:26:25.437][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 20:26:25.439][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 20:26:25.441][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 20:26:25.443][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 20:26:25.445][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 20:26:25.447][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 20:26:25.449][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 20:26:25.451][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 20:26:25.453][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 20:26:25.455][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 20:26:25.457][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 20:26:25.458][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 20:26:25.461][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 20:26:25.463][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 20:26:25.465][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 20:26:25.467][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 20:26:25.477][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 20:26:25.479][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 20:26:25.481][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 20:26:25.483][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 20:26:25.485][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 20:26:25.488][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 20:26:25.490][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 20:26:25.492][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 20:26:25.494][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 20:26:25.496][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 20:26:25.498][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 20:26:25.499][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 20:26:25.501][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 20:26:25.503][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:26:25.505][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:26:25.507][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 20:26:25.509][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 20:26:25.511][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 20:26:25.513][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 20:26:25.515][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 20:26:25.517][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 20:26:25.519][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 20:26:25.521][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 20:26:25.523][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 20:26:25.525][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 20:26:25.527][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 20:26:25.530][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 20:26:25.532][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 20:26:25.534][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 20:26:25.536][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 20:26:25.545][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 20:26:25.548][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:26:25.554][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:26:25.555][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.558][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.560][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[2024-05-03 20:26:25.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.611][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[2024-05-03 20:26:25.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.621][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[2024-05-03 20:26:25.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.666][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[2024-05-03 20:26:25.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.677][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:25.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:26:25.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.726][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[2024-05-03 20:26:25.729][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-03 20:26:25.743][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-03 20:26:25.746][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.748][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.750][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.751][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:26:25.753][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.756][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.757][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-03 20:26:25.758][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-03 20:26:25.760][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:26:25.762][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.771][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-03 20:26:25.773][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-03 20:26:25.775][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-03 20:26:25.777][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 20:26:25.778][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:26:25.778][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:26:25.778][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:26:25.780][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-03 20:26:25.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.783][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:26:25.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:26:25.786][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:26:25.787][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:26:25.789][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:25.789][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-03 20:26:25.790][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:26:25.792][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:26:25.793][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 20:26:25.795][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-03 20:26:25.795][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-03 20:26:25.804][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:26:25.806][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:26:25.808][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-03 20:26:25.810][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:26:25.812][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:26:25.815][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:26:25.852][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-03 20:26:25.854][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-03 20:26:25.860][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-03 20:26:25.866][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-03 20:26:25.872][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 20:26:25.874][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 20:26:25.876][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-03 20:26:25.877][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-03 20:26:25.891][biodb::testThat]
biodb.INFO [2024-05-03 20:26:25.893][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-05-03 20:26:25.895][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:25.896][biodb::testThat]
biodb.TRACE[2024-05-03 20:26:25.903][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-05-03 20:26:25.906][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:25.911][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:25.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:25.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:25.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:25.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:25.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:25.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:25.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:25.964][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:25.966][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:25.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:25.969][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:25.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:25.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:25.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:25.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:25.996][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:25.998][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:25.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.001][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.040][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:26.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:26.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.047][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:26.049][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:26.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.052][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:26.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:26.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.060][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:26.061][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:26.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.064][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:26.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:26.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.072][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.073][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.076][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.084][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.085][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.101][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.103][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.110][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:26.111][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.114][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.116][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:26.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.122][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.123][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.126][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.133][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:26.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:26.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.137][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:26.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:26.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.144][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:26.145][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.148][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.149][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:26.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.155][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:26.156][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:26.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.159][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.161][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:26.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:26.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:26.274][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-05-03 20:26:26.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:26.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:26.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:26.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:26.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.392][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:26:26.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:26:26.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.401][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:26:26.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:26:26.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.410][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 20:26:26.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 20:26:26.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.415][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 20:26:26.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 20:26:26.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.551][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.552][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.555][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:26.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:26.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.591][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.592][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.594][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:26.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.621][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:26.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:26.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:26.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:26.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:26.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:26.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.636][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:26.637][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:26.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.639][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:26.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:26.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.657][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:26.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:26.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.662][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:26.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:26.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.668][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:26.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:26.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.672][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:26.674][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:26.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.676][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:26.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:26.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.713][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.715][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.717][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:26.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.763][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:26.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.784][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:26.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:26.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.791][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.797][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:26.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:26.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.802][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:26.804][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:26.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.806][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.808][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:26.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:26.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.827][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.833][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.838][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.844][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.845][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.856][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:26.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.874][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.880][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.885][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.890][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.892][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.895][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.896][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:26.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.918][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:26.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:26.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.925][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:26.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:26.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:26.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:26.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.944][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:26.947][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:26.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.950][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.952][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:26.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:26.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:26.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:26.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:26.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.021][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.041][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.044][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.048][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:27.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:27.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.088][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:27.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:27.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:27.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:27.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.115][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:27.117][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:27.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.121][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:27.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:27.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.153][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:27.173][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:27.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.177][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.191][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:27.193][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:27.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.195][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.218][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:27.220][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:27.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.223][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.247][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:27.249][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:27.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.252][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.264][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.266][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.269][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.292][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:27.293][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:27.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.308][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.316][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:27.317][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:27.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.320][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.328][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:27.330][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:27.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.356][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-05-03 20:26:27.358][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:27.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.360][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.387][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:27.389][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:27.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.392][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.406][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:27.408][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:27.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.411][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 20:26:27.441][biodb::testThat]
biodb.INFO [2024-05-03 20:26:27.442][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-05-03 20:26:27.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:27.445][biodb::testThat]
biodb.DEBUG[2024-05-03 20:26:27.489][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-05-03 20:26:27.510][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:27.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-05-03 20:26:27.519][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:26:27.531][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-05-03 20:26:27.533][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:27.610][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:27.612][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:27.615][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:27.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:27.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:27.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:27.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:27.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:27.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:27.660][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:27.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:27.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.666][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:27.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:27.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.733][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:27.735][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:27.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.738][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.826][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:27.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:27.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.842][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:27.845][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:27.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.848][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:27.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:27.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.862][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:27.864][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:27.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.878][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.880][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:27.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:27.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.897][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.900][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:27.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.924][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:27.926][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:27.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.928][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.935][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:27.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:27.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.942][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:27.950][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:27.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.953][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.955][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:27.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:27.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.975][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:27.977][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:27.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.980][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:27.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:27.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:27.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:27.997][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:27.999][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:28.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.010][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:28.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:28.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.027][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:28.029][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:28.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.033][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.045][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:28.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.053][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:28.062][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:28.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.065][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.068][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:28.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:28.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:28.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:28.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:28.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:28.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:28.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:28.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:28.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:28.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:28.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:28.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:28.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:28.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:28.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:28.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:28.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:28.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:28.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:28.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:28.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:28.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:28.230][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-05-03 20:26:28.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-05-03 20:26:28.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-05-03 20:26:28.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-05-03 20:26:28.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-05-03 20:26:28.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-05-03 20:26:28.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-05-03 20:26:28.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:26:28.321][biodb::testThat]
biodb.INFO [2024-05-03 20:26:28.324][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-05-03 20:26:28.325][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:28.327][biodb::testThat]
biodb.TRACE[2024-05-03 20:26:28.342][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:28.344][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:28.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.352][ef$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:28.355][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-05-03 20:26:28.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:28.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:28.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:28.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:28.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:28.482][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:28.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:28.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:28.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:28.500][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-05-03 20:26:28.514][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-03 20:26:28.566][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:26:28.611][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-03 20:26:28.613][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:26:28.616][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-03 20:26:28.680][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[2024-05-03 20:26:28.691][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:28.694][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:28.697][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-03 20:26:29.890][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-03 20:26:30.742][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:30.747][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-05-03 20:26:30.771][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-05-03 20:26:30.774][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-05-03 20:26:30.796][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:30.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:30.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:30.801][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:30.802][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:30.804][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:30.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:30.807][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 20:26:30.814][biodb::testThat]
biodb.INFO [2024-05-03 20:26:30.833][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-05-03 20:26:30.835][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:30.836][biodb::testThat]
biodb.TRACE[2024-05-03 20:26:30.874][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:30.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:30.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:30.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:30.881][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:30.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:30.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:30.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:30.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:30.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:30.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:30.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:30.990][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:26:30.999][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:26:31.001][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 20:26:31.003][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:26:31.006][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-05-03 20:26:31.062][biodb::testThat]
biodb.INFO [2024-05-03 20:26:31.064][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-05-03 20:26:31.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:31.067][biodb::testThat]
biodb.TRACE[2024-05-03 20:26:31.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:31.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:31.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:31.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:31.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:31.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:31.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.175][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:31.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:31.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:31.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:31.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:31.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:31.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.210][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:26:31.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:26:31.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.224][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:26:31.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:26:31.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.231][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 20:26:31.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 20:26:31.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.247][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 20:26:31.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 20:26:31.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:31.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:31.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.323][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:31.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:31.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:31.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:31.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:31.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:31.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:31.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:31.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:31.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:31.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.384][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:26:31.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:26:31.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.401][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-05-03 20:26:31.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-05-03 20:26:31.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.416][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-05-03 20:26:31.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-05-03 20:26:31.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:31.443][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-05-03 20:26:31.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-05-03 20:26:31.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:31.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:26:31.479][biodb::testThat]
biodb.INFO [2024-05-03 20:26:31.481][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-05-03 20:26:31.482][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:31.484][biodb::testThat]
biodb.INFO [2024-05-03 20:26:31.502][biodb::testThat]
biodb.INFO [2024-05-03 20:26:31.503][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-05-03 20:26:31.505][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:31.507][biodb::testThat]
biodb.INFO [2024-05-03 20:26:31.539][biodb::testThat]
biodb.INFO [2024-05-03 20:26:31.541][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-05-03 20:26:31.542][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:31.544][biodb::testThat]
biodb.DEBUG[2024-05-03 20:26:31.558][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-05-03 20:26:32.228][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-05-03 20:26:33.567][biodb::testThat]
biodb.INFO [2024-05-03 20:26:33.569][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-05-03 20:26:33.571][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:33.572][biodb::testThat]
biodb.DEBUG[2024-05-03 20:26:34.031][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[2024-05-03 20:26:34.487][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:34.488][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:34.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.491][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:34.493][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:34.494][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:34.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.497][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 20:26:34.500][biodb::testThat]
biodb.INFO [2024-05-03 20:26:34.501][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-05-03 20:26:34.502][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:26:34.504][biodb::testThat]
biodb.TRACE[2024-05-03 20:26:34.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:34.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:34.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:34.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:34.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:34.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:34.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:34.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:34.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:34.675][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:26:34.680][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:26:34.682][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 20:26:34.684][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:26:34.687][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 20:26:34.844][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:26:34.849][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:26:34.851][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 20:26:34.853][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:26:34.863][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-05-03 20:26:34.889][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 20:26:34.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 20:26:34.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:34.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:34.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:34.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:34.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:34.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:34.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:34.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:35.002][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:26:35.054][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:35.055][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:35.103][private$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[2024-05-03 20:26:35.642][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[2024-05-03 20:26:36.056][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:36.059][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-05-03 20:26:36.065][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-05-03 20:26:36.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:36.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:36.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:36.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:36.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:36.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:36.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:36.101][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-05-03 20:26:36.170][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:36.173][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-05-03 20:26:36.175][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:36.177][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:36.179][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:36.181][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:36.182][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:36.184][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:36.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:36.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:36.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:36.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:36.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:36.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:36.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:36.206][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-05-03 20:26:36.211][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:36.212][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:36.214][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-05-03 20:26:36.638][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-05-03 20:26:37.053][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:37.056][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-05-03 20:26:37.061][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-05-03 20:26:37.066][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-05-03 20:26:37.068][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:37.070][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:37.072][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:37.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:37.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:37.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:37.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:37.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:37.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:37.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:37.106][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.108][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.111][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.118][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:37.120][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:37.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.122][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.124][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:37.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:37.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.130][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:37.131][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:37.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.134][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.136][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:37.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:37.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.142][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:37.143][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:37.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.146][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:37.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:37.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.153][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:37.154][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:37.155][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.157][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:37.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:37.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.164][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:37.165][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:37.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.168][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.169][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:37.171][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:37.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.173][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.175][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:37.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:37.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.181][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:37.183][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:37.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.185][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:37.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:37.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.192][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:37.194][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:37.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.197][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:37.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:37.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.205][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:37.206][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:37.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.209][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.211][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:37.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:37.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.216][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:37.218][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:37.219][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.220][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.222][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:37.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:37.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:37.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:37.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:37.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:37.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:37.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:37.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:37.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:37.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:37.313][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-05-03 20:26:37.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:37.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:37.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:37.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:37.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:37.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:37.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:37.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:37.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:37.373][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[2024-05-03 20:26:37.385][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:37.387][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:37.390][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-03 20:26:37.822][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-03 20:26:38.237][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:38.241][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-05-03 20:26:38.249][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-05-03 20:26:38.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:38.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:38.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:38.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:38.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:38.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:38.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:38.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:38.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:38.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:38.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:38.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:38.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:38.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:38.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:38.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:38.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:38.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:38.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:38.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:38.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:38.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:38.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:38.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:38.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:38.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:38.345][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-05-03 20:26:38.347][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:38.349][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-05-03 20:26:38.365][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:38.372][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:38.375][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:38.376][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:38.379][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:38.380][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:38.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:38.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:38.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:38.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:38.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:38.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:38.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:38.425][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-05-03 20:26:38.430][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:38.433][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:38.435][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-05-03 20:26:38.867][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-05-03 20:26:39.288][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:39.294][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-05-03 20:26:39.302][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-05-03 20:26:39.308][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-05-03 20:26:39.312][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:39.314][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:39.316][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:39.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:39.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:39.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:39.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:39.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:39.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:39.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:39.346][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.348][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.351][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.362][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:39.364][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:39.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.368][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.371][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:39.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:39.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.379][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:39.381][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:39.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.385][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.387][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:39.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:39.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.395][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:39.396][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:39.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.399][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:39.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:39.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.408][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:39.410][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:39.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.413][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:39.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:39.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.422][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:39.424][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:39.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.427][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.429][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:39.431][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.459][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.463][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:39.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:39.474][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:39.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:39.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:39.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.488][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:39.489][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:39.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.493][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.496][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:39.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:39.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.505][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:39.512][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:39.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.517][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.520][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:39.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:39.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.533][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:39.539][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:39.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.544][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.546][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:39.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:39.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:39.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:39.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:39.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:39.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:39.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:39.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:39.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:39.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:39.725][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-05-03 20:26:39.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:39.823][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:26:39.834][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:26:39.836][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 20:26:39.861][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:26:39.863][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 20:26:39.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:39.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:39.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:39.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:39.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:39.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:39.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:39.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:39.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:39.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:39.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:39.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:39.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:39.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:39.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:39.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:39.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:39.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:39.964][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-05-03 20:26:39.972][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:39.975][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-05-03 20:26:39.977][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:39.978][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:39.980][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:39.986][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:39.988][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:39.990][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:39.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:39.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:40.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:40.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:40.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:40.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:40.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:40.025][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-05-03 20:26:40.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:40.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:40.057][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-05-03 20:26:40.476][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-05-03 20:26:40.897][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:40.900][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-05-03 20:26:40.906][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-05-03 20:26:40.910][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-05-03 20:26:40.913][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:40.914][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:40.916][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:40.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:40.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:40.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:40.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:40.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:40.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:40.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:40.937][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:40.939][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:40.941][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:40.942][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:40.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:40.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:40.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:40.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:40.950][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:40.951][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:40.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:40.954][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:40.956][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:40.957][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:40.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:40.960][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:40.962][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:40.963][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:40.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:40.966][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:40.967][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:40.969][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:40.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:40.985][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:40.987][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:40.989][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:40.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:40.992][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:40.994][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:40.995][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:40.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:40.998][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.000][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:41.001][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:41.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.004][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.005][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:41.007][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:41.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.010][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:41.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:41.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.018][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:41.019][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:41.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.022][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.023][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:41.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:41.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.029][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:41.031][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:41.032][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.033][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:41.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:41.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:41.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:41.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:41.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:41.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:41.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:41.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:41.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:41.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:41.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:41.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:41.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:41.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:41.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:41.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.079][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:41.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:41.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:41.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:41.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:41.094][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-05-03 20:26:41.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:41.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:41.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:41.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:41.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:41.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:41.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:41.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:41.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:41.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:41.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:41.141][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-05-03 20:26:41.147][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:41.149][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-05-03 20:26:41.152][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:41.153][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:41.171][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:41.179][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:41.181][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:41.182][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:41.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:41.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:41.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:41.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:41.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:41.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:41.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:41.222][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-05-03 20:26:41.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:41.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:41.233][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-05-03 20:26:41.666][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-05-03 20:26:42.081][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:42.086][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-05-03 20:26:42.093][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-05-03 20:26:42.098][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-05-03 20:26:42.101][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:42.104][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:42.106][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:42.109][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:42.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:42.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:42.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:42.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:42.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:42.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:42.133][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.135][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.138][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.147][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:42.149][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:42.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.152][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.154][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:42.156][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:42.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.159][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.161][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:42.163][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:42.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.166][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.168][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:42.170][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:42.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.173][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.176][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:42.177][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:42.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.181][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.183][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:42.185][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.188][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.190][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:42.192][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:42.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.195][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.197][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:42.199][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:42.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.202][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.204][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:42.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:42.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.211][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:42.213][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:42.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.216][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.218][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:42.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:42.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.224][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:42.226][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:42.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.229][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:42.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:42.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:42.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:42.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:42.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:42.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:42.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:42.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:42.352][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-05-03 20:26:42.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:42.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:42.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:42.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:42.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:42.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:42.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:42.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:42.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:42.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:42.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:42.473][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-05-03 20:26:42.475][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:42.478][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-05-03 20:26:42.486][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:42.489][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:42.491][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:42.493][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:42.498][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:42.500][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:42.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:42.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:42.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:42.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:42.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:42.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:42.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:42.547][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-05-03 20:26:42.554][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:42.561][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:42.565][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-05-03 20:26:43.007][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-05-03 20:26:43.419][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:43.422][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-05-03 20:26:43.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-05-03 20:26:43.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-05-03 20:26:43.434][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:43.436][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:43.438][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:43.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:43.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:43.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:43.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:43.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:43.495][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:43.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:43.500][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.502][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.504][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.512][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:43.513][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:43.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.516][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.518][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:43.519][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:43.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.522][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.524][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:43.525][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:43.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.528][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.529][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:43.531][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:43.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.533][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.535][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:43.537][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:43.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.539][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.541][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:43.543][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.545][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.547][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:43.548][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:43.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.551][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.552][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:43.554][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:43.555][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.556][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:43.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:43.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.564][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:43.565][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:43.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.568][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.570][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:43.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:43.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.576][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:43.577][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:43.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.580][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:43.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:43.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:43.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:43.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:43.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:43.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:43.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:43.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:43.639][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-05-03 20:26:43.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:43.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:43.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:43.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:43.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:43.722][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:43.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:43.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:43.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:43.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:43.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:43.738][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-05-03 20:26:43.748][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:43.751][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-05-03 20:26:43.753][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:43.755][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:43.772][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:43.776][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:43.778][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:43.780][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:43.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:43.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:43.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:43.807][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:43.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:43.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:43.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:43.822][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-05-03 20:26:43.827][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:43.829][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:43.838][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-05-03 20:26:44.296][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-05-03 20:26:44.712][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:44.715][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-05-03 20:26:44.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-05-03 20:26:44.725][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-05-03 20:26:44.728][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:44.730][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:44.732][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:44.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:44.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:44.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:44.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:44.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:44.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:44.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:44.753][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:44.754][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:44.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.757][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:44.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:44.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.765][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:44.767][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:44.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.771][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:44.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:44.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.777][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:44.778][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:44.780][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.781][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:44.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:44.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.789][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:44.791][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:44.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.794][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:44.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:44.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.801][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:44.803][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:44.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.805][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:44.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:44.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.826][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:44.828][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:44.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.831][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.833][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:44.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:44.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.839][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:44.840][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:44.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.843][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.845][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:44.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:44.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.850][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:44.852][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:44.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.855][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:44.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:44.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.863][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:44.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:44.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.867][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.869][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:44.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:44.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.876][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:44.877][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:44.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.880][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.882][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:44.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:44.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.887][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:44.889][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:44.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.891][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.895][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:44.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:44.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:44.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:44.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:44.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:44.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:44.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:44.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:44.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:44.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:44.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:44.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:44.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:44.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:44.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:44.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:44.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:44.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:44.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:44.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:44.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:44.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:45.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:45.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:45.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:45.013][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-05-03 20:26:45.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:45.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:45.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:45.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:45.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:45.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:45.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:45.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:45.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:45.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:45.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:45.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:45.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:45.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:45.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:45.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:45.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:45.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:45.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:45.097][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-05-03 20:26:45.099][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:45.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-05-03 20:26:45.104][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:45.113][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:45.115][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:45.118][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:45.120][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:45.121][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:45.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:45.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:45.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:45.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:45.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:45.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:45.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:45.173][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-05-03 20:26:45.178][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:45.180][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:45.182][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-05-03 20:26:45.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-05-03 20:26:46.073][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:46.076][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-05-03 20:26:46.081][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-05-03 20:26:46.084][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-05-03 20:26:46.086][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:46.088][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:46.089][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:46.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:46.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:46.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:46.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:46.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:46.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:46.104][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[2024-05-03 20:26:46.108][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.109][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.112][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.119][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:46.121][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:46.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.125][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:46.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:46.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.130][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:46.131][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:46.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.133][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:46.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:46.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.140][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:46.141][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:46.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.144][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.145][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:46.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:46.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.151][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:46.153][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:46.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.155][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:46.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:46.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.162][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:46.164][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:46.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.166][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.168][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:46.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:46.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.173][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:46.175][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:46.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.177][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.179][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:46.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:46.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.190][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:46.196][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:46.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.199][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:46.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:46.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.205][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:46.206][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:46.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.208][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:46.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:46.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.215][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:46.216][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:46.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.218][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.219][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:46.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:46.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.223][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:46.224][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:46.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.226][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.227][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:46.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:46.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:46.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:46.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:46.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:46.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:46.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:46.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:46.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:46.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:46.277][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-05-03 20:26:46.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:46.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:46.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:46.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:46.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:46.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:46.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:46.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:46.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:46.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:46.293][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:46.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:46.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:46.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:46.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:46.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:46.305][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-05-03 20:26:46.306][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:46.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-05-03 20:26:46.310][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:46.311][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:46.313][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:46.314][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:46.316][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:46.317][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:46.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:46.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:46.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:46.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:46.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:46.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:46.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:46.343][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-05-03 20:26:46.346][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:46.347][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:46.349][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-05-03 20:26:46.768][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-05-03 20:26:47.184][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:47.188][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-05-03 20:26:47.194][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-05-03 20:26:47.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-05-03 20:26:47.201][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:47.203][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:47.205][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:47.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:47.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:47.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:47.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:47.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:47.223][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:47.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:47.228][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.230][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.233][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.241][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:47.242][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:47.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.245][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.247][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:47.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:47.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.253][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:47.254][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:47.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.257][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.259][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:47.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:47.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.265][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:47.266][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:47.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.269][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:47.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:47.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.277][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:47.278][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:47.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.281][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.283][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:47.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:47.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.289][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:47.290][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:47.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.293][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.295][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:47.296][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:47.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.299][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.300][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:47.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:47.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.306][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:47.308][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:47.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.311][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:47.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:47.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.318][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:47.320][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:47.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.322][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:47.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:47.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.328][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:47.330][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:47.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.332][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.333][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:47.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:47.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.351][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:47.353][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:47.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.357][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.359][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:47.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:47.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:47.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:47.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:47.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:47.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:47.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:47.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:47.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:47.419][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-05-03 20:26:47.420][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:47.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:47.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:47.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:47.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:47.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:47.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:47.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:47.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:47.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:47.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:47.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:47.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:47.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:47.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:47.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:47.452][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-05-03 20:26:47.453][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:47.456][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-05-03 20:26:47.458][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:47.459][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:47.461][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:47.463][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:47.467][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:47.469][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:47.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:47.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:47.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:47.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:47.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:47.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:47.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:47.499][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-05-03 20:26:47.507][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:47.509][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:47.511][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-05-03 20:26:47.942][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-05-03 20:26:48.350][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:48.353][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-05-03 20:26:48.357][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-05-03 20:26:48.360][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-05-03 20:26:48.362][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:48.364][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:48.371][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:48.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:48.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:48.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:48.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:48.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:48.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:48.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:48.395][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.396][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.398][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.404][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:48.405][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:48.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.407][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.409][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:48.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:48.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.414][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:48.416][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:48.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.419][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:48.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:48.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.426][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:48.428][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:48.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.430][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.432][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:48.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:48.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.436][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:48.437][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:48.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.439][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:48.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:48.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.445][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:48.446][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:48.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.448][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.450][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:48.451][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:48.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.454][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.455][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:48.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:48.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.461][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:48.462][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:48.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.464][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:48.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:48.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.471][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:48.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:48.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.475][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:48.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:48.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.483][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:48.484][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:48.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.486][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.488][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:48.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:48.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.493][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:48.495][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:48.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.499][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:48.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:48.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:48.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:48.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:48.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:48.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:48.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:48.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:48.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:48.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:48.559][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-05-03 20:26:48.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:48.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:48.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:48.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:48.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:48.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:48.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:48.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:48.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:48.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:48.572][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:48.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:48.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:48.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:48.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:48.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:48.586][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-05-03 20:26:48.589][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:48.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-05-03 20:26:48.594][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:48.595][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:48.597][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:48.600][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:48.602][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:48.603][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:48.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:48.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:48.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:48.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:48.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:48.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:48.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:48.692][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-05-03 20:26:48.696][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:48.698][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:48.700][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-05-03 20:26:49.117][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-05-03 20:26:49.527][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:49.530][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-05-03 20:26:49.536][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-05-03 20:26:49.540][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-05-03 20:26:49.542][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:49.544][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:49.546][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:49.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:49.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:49.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:49.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:49.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:49.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:49.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:49.567][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.571][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.578][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:49.580][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:49.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.597][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.599][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:49.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:49.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.605][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:49.607][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:49.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.610][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.611][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:49.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:49.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.617][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:49.619][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:49.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.621][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:49.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:49.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.629][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:49.630][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:49.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.633][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:49.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:49.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.641][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:49.642][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:49.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.645][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.647][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:49.649][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:49.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.651][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.653][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:49.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:49.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.660][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:49.662][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:49.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.665][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:49.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:49.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.673][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:49.675][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:49.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.678][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:49.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:49.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.687][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:49.689][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:49.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.692][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.694][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:49.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:49.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.700][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:49.702][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:49.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.705][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.707][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:49.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:49.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:49.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:49.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:49.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:49.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:49.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:49.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:49.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:49.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:49.824][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-05-03 20:26:49.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:49.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:49.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:49.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:49.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:49.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:49.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:49.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:49.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:49.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:49.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:49.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:49.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:49.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:49.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:49.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:49.896][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-05-03 20:26:49.898][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:49.902][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-05-03 20:26:49.909][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:49.911][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:49.914][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:49.916][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:49.924][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:49.927][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:49.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:49.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:49.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:49.968][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:49.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:49.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:49.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:49.985][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-05-03 20:26:49.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:49.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:50.001][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-05-03 20:26:50.424][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-05-03 20:26:50.844][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:50.847][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-05-03 20:26:50.853][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-05-03 20:26:50.857][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-05-03 20:26:50.859][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:50.861][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:50.863][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:50.866][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:50.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:50.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:50.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:50.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:50.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:50.881][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[2024-05-03 20:26:50.884][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:50.886][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:50.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.889][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:50.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:50.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.896][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:50.898][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:50.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.900][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.902][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:50.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:50.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.908][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:50.909][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:50.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.912][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.913][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:50.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:50.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.919][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:50.920][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:50.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.923][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:50.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:50.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.943][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:50.945][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:50.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.948][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:50.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:50.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.955][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:50.957][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:50.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.959][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.961][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:50.963][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:50.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.965][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.967][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:50.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.972][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:50.974][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:50.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.976][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:50.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:50.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.984][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:50.985][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:50.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.988][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:50.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:50.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:50.995][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:50.996][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:50.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:50.999][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.001][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:51.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:51.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.006][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:51.008][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:51.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.010][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.012][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:51.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:51.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:51.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:51.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:51.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:51.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:51.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:51.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:51.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:51.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:51.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:51.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:51.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:51.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:51.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:51.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:51.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:51.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:51.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:51.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:51.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:51.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:51.093][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-05-03 20:26:51.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:51.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:51.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:51.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:51.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:51.109][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:51.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:51.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:51.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:51.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:51.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:51.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:51.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:51.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:51.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:51.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:51.144][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-05-03 20:26:51.152][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:51.156][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-05-03 20:26:51.158][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:51.160][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:51.169][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:51.172][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:51.174][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:51.175][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:51.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:51.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:51.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:51.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:51.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:51.213][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:51.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:51.226][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-05-03 20:26:51.231][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:51.233][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:51.235][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-05-03 20:26:51.663][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-05-03 20:26:52.081][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:52.086][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-05-03 20:26:52.092][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-05-03 20:26:52.098][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-05-03 20:26:52.101][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:52.104][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:52.107][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:52.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:52.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:52.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:52.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:52.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:52.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:52.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:52.134][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.136][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.140][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.150][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:52.152][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:52.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.155][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.157][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:52.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:52.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.164][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:52.167][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:52.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.170][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.172][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:52.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:52.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.180][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:52.181][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:52.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.185][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.187][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:52.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:52.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.194][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:52.196][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:52.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.199][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:52.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:52.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.208][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:52.210][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:52.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.213][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.216][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:52.218][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:52.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.221][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.224][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:52.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:52.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.249][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:52.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:52.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.264][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:52.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:52.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.274][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:52.276][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:52.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.279][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:52.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:52.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.287][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:52.288][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:52.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.291][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.292][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:52.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:52.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.298][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:52.299][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:52.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.310][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.313][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:52.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:52.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:52.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:52.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:52.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:52.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:52.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:52.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:52.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:52.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:52.431][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-05-03 20:26:52.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:52.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:52.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:52.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:52.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:52.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:52.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:52.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:52.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:52.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:52.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:52.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:52.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:52.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:52.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:52.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:52.488][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-05-03 20:26:52.502][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:52.505][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-05-03 20:26:52.507][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:52.510][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:52.520][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:52.522][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:52.524][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:52.526][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:52.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:52.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:52.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:52.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:52.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:52.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:52.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:52.582][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-05-03 20:26:52.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:52.589][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:52.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-05-03 20:26:53.020][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-05-03 20:26:53.433][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:53.436][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-05-03 20:26:53.441][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-05-03 20:26:53.446][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-05-03 20:26:53.448][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:53.450][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:53.452][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:53.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:53.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:53.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:53.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:53.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:53.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:53.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:53.473][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.474][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.485][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:53.486][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:53.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.489][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.490][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:53.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:53.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.497][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:53.498][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:53.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.501][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:53.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:53.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.508][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:53.510][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:53.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.512][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.514][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:53.515][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:53.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.518][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.519][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:53.521][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:53.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.524][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.526][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:53.527][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:53.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.530][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:53.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.538][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:53.539][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:53.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.542][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:53.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:53.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.549][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:53.551][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:53.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.553][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:53.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:53.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.561][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:53.563][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:53.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.565][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.567][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:53.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:53.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.573][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:53.574][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:53.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.577][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:53.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:53.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:53.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:53.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:53.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:53.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:53.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:53.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:53.670][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-05-03 20:26:53.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:53.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:53.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:53.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:53.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:53.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:53.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:53.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:53.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:53.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:53.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:53.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:53.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:53.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:53.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:53.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:53.721][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-05-03 20:26:53.730][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:53.732][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-05-03 20:26:53.734][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:53.736][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:53.738][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:53.746][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:53.748][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:53.749][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:53.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:53.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:53.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:53.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:53.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:53.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:53.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:53.787][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-05-03 20:26:53.798][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:53.799][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:53.802][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-05-03 20:26:54.262][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-05-03 20:26:54.674][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:54.679][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-05-03 20:26:54.685][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-05-03 20:26:54.691][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-05-03 20:26:54.694][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:54.696][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:54.699][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:54.702][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:54.703][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:54.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:54.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:54.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:54.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:54.743][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.TRACE[2024-05-03 20:26:54.748][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.750][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.754][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.763][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:54.764][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:54.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.767][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.769][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:54.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:54.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.775][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:54.777][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:54.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.780][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:54.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:54.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.788][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:54.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:54.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.792][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.794][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:54.796][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:54.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.799][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.800][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:54.802][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:54.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.805][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.807][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:54.808][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:54.810][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.811][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.813][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.819][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:54.821][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:54.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.823][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:54.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:54.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.831][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:54.833][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:54.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.836][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.838][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:54.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:54.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.844][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:54.846][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:54.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.849][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.850][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:54.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:54.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.856][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:54.858][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:54.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.861][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:54.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:54.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:54.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:54.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:54.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:54.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:54.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:54.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:54.972][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-05-03 20:26:54.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:54.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:54.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:54.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:54.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:54.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:54.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:55.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:55.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:55.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:55.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:55.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:55.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:55.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:55.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:55.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:55.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:55.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:55.043][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-05-03 20:26:55.045][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:55.048][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-05-03 20:26:55.050][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:55.060][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:55.063][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:55.065][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:55.067][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:55.069][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:55.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:55.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:55.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:55.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:55.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:55.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:55.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:55.121][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-05-03 20:26:55.126][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:55.135][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:55.139][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-05-03 20:26:55.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-05-03 20:26:55.972][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:55.975][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-05-03 20:26:55.981][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-05-03 20:26:55.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-05-03 20:26:55.988][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:55.990][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:55.992][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:55.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:55.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:55.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:56.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:56.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:56.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:56.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:56.013][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.014][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.017][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.025][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:56.027][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:56.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.029][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.031][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:56.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:56.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.038][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:56.040][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:56.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.043][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.046][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:56.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:56.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:56.054][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:56.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.070][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:56.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:56.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.079][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:56.080][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:56.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.083][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:56.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:56.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.090][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:56.092][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:56.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.095][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.096][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:56.098][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:56.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.101][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.102][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:56.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:56.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.108][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:56.110][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:56.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.112][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:56.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:56.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.120][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:56.122][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:56.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.124][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:56.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:56.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.132][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:56.134][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:56.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.137][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.139][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:56.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:56.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.145][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:56.146][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:56.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.149][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.151][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:56.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:56.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:56.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:56.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:56.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:56.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:56.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:56.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:56.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:56.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:56.250][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-05-03 20:26:56.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:56.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:56.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:56.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:56.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:56.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:56.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:56.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:56.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:56.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:56.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:56.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:56.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:56.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:56.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:56.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:56.337][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-05-03 20:26:56.344][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:56.348][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-05-03 20:26:56.350][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:56.352][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:56.360][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:56.362][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:56.364][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:56.366][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:56.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:56.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:56.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:56.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:56.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:56.392][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:56.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:56.396][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-05-03 20:26:56.407][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:56.408][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:56.410][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-05-03 20:26:56.850][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-05-03 20:26:57.264][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:57.268][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-05-03 20:26:57.273][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-05-03 20:26:57.277][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-05-03 20:26:57.279][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:57.281][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:57.283][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:57.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:57.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:57.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:57.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:57.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:57.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:57.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:57.303][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.304][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.307][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.315][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:57.316][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:57.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.319][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.321][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:57.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:57.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.326][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:57.328][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:57.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.330][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.332][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:57.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:57.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.338][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:57.339][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:57.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.342][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:57.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:57.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.349][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:57.351][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:57.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.354][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:57.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:57.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.361][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:57.362][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:57.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.365][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.367][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:57.382][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:57.384][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.385][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.387][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:57.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:57.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.393][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:57.394][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:57.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.397][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:57.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:57.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.404][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:57.405][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:57.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.408][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:57.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.415][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:57.417][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:57.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.419][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.421][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:57.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:57.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.427][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:57.428][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:57.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.431][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.432][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:57.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:57.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:57.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:57.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:57.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:57.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:57.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:57.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:57.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:57.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:57.524][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-05-03 20:26:57.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:57.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:57.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:57.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:57.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:57.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:57.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:57.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:57.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:57.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:57.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:57.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:57.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:57.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:57.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:57.573][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-05-03 20:26:57.582][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:57.585][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-05-03 20:26:57.588][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:57.589][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:57.591][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:57.621][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:57.623][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:57.625][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:57.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:57.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:57.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:57.648][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:57.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:57.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:57.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:57.654][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-05-03 20:26:57.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:57.683][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:57.686][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-05-03 20:26:58.137][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-05-03 20:26:58.548][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:58.551][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-05-03 20:26:58.557][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-05-03 20:26:58.561][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-05-03 20:26:58.563][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:58.565][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:58.567][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:58.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:58.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:58.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:58.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:58.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:58.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:58.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:58.588][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.589][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.592][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.599][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:58.600][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:58.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.603][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.604][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:58.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:58.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.610][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:58.611][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:58.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.614][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.615][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:58.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:58.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.621][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:58.622][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:58.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.625][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:58.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:58.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.632][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:58.633][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:58.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.636][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:58.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:58.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.643][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:58.645][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:58.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.648][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.649][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:58.651][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:58.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.653][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.655][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:58.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:58.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.661][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:58.662][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:58.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.665][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:58.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:58.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.673][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:58.674][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:58.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.677][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:58.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:58.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.699][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:58.701][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:58.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.704][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.705][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:58.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:58.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.711][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:58.713][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:58.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.717][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:26:58.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:26:58.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:58.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:58.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:58.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:58.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:26:58.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:26:58.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:58.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:58.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:58.815][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-05-03 20:26:58.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:58.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:58.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:58.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:58.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:58.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:58.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:58.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:58.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:26:58.853][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:58.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:58.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:58.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:58.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:58.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:58.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:58.869][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-05-03 20:26:58.870][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:26:58.886][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-05-03 20:26:58.888][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:26:58.890][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:26:58.892][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:26:58.900][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:26:58.902][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:26:58.904][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:26:58.908][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:58.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:58.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:58.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:58.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:58.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:58.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:26:58.937][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-05-03 20:26:58.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:26:58.949][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:26:58.951][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-05-03 20:26:59.418][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-05-03 20:26:59.840][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:26:59.844][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-05-03 20:26:59.850][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-05-03 20:26:59.855][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-05-03 20:26:59.857][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:26:59.859][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:26:59.861][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:26:59.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:26:59.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:26:59.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:26:59.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:26:59.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:26:59.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:26:59.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:26:59.884][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:59.886][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:59.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.889][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:26:59.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:26:59.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.898][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:59.899][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:59.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.902][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.904][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:26:59.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:26:59.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.910][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:59.912][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:59.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.915][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.917][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:26:59.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:26:59.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.923][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:59.925][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:59.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.927][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.929][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:26:59.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:26:59.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.935][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:59.937][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:59.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.940][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:26:59.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:26:59.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.947][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:59.949][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:26:59.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.952][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.954][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:59.956][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:59.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.958][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:26:59.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:26:59.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.966][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:59.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:59.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.971][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:59.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:26:59.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.979][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:59.981][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:59.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.984][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:26:59.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:26:59.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:26:59.993][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:26:59.994][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:26:59.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:26:59.997][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.000][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:00.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:00.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.006][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:00.008][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:00.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.011][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.013][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:00.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:00.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:00.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:00.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:00.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:00.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:00.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:00.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:00.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:00.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:00.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:00.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:00.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:00.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:00.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:00.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:00.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:00.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:00.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:00.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:00.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:00.177][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-05-03 20:27:00.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:00.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:00.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:00.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:00.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:00.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:00.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:00.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:00.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:00.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:00.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:00.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:00.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:00.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:00.245][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:00.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:00.268][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-05-03 20:27:00.270][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:27:00.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-05-03 20:27:00.284][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:27:00.286][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:27:00.289][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:00.291][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:27:00.304][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:27:00.306][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:27:00.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:00.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:00.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:00.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:00.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:00.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:00.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:00.357][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-05-03 20:27:00.362][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:00.364][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:00.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-05-03 20:27:00.798][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-05-03 20:27:01.215][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:01.220][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-05-03 20:27:01.227][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-05-03 20:27:01.233][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-05-03 20:27:01.236][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:27:01.239][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:27:01.241][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:27:01.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:01.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:01.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:01.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:01.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:01.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:01.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:01.297][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.300][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.304][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.314][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:01.316][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:01.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.319][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.322][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:01.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:01.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.329][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:01.331][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:01.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.334][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:01.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:01.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.343][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:01.344][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:01.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.347][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.350][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:01.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:01.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.357][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:01.358][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:01.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.361][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:01.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:01.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.372][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:01.374][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:01.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.377][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.379][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:01.380][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:01.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.383][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.386][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:01.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:01.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.393][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:01.395][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:01.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.398][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:01.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:01.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.410][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:01.412][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:01.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.415][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:01.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:01.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.435][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:01.438][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:01.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.441][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.444][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:01.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:01.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.467][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:01.470][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:01.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.475][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.485][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:01.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:01.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:01.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:01.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:01.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:01.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:01.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:01.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:01.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:01.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:01.675][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-05-03 20:27:01.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:01.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:01.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:01.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:01.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:01.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:01.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:01.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:01.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:01.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:01.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:01.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:01.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:01.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:01.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:01.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:01.736][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-05-03 20:27:01.742][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:27:01.745][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-05-03 20:27:01.747][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:27:01.749][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:27:01.751][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:01.760][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:27:01.762][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:27:01.763][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:27:01.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:01.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:01.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:01.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:01.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:01.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:01.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:01.814][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-05-03 20:27:01.838][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:01.839][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:01.843][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-05-03 20:27:02.269][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-05-03 20:27:02.681][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:02.685][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-05-03 20:27:02.690][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-05-03 20:27:02.693][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-05-03 20:27:02.696][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:27:02.698][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:27:02.699][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:27:02.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:02.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:02.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:02.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:02.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:02.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:02.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:02.718][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.720][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.722][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.730][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:02.731][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:02.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.734][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.736][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:02.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:02.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.740][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:02.752][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:02.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.755][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.758][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:02.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:02.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.767][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:02.769][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:02.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.771][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:02.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:02.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.778][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:02.780][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:02.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.782][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:02.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:02.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.789][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:02.791][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:02.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.793][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.795][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:02.801][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:02.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.804][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.806][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:02.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:02.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.816][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:02.818][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:02.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.822][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:02.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:02.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.838][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:02.840][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:02.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.847][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:02.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:02.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.855][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:02.856][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:02.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.859][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.860][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:02.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:02.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.866][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:02.868][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:02.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.870][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.872][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:02.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:02.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:02.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:02.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:02.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:02.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:02.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:02.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:02.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:02.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:02.933][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-05-03 20:27:02.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:02.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:02.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.959][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:02.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:02.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:02.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:02.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:02.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:02.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:02.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:02.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:02.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:02.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:02.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:03.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:03.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:03.022][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-05-03 20:27:03.024][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:27:03.027][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-05-03 20:27:03.029][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:27:03.032][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:27:03.033][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:03.035][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:27:03.036][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:27:03.038][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:27:03.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:03.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:03.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:03.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:03.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:03.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:03.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:03.073][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-05-03 20:27:03.081][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:03.082][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:03.085][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-05-03 20:27:03.526][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-05-03 20:27:03.944][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:03.948][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-05-03 20:27:03.954][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-05-03 20:27:03.960][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-05-03 20:27:03.963][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:27:03.966][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:27:03.972][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:27:03.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:03.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:03.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:03.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:03.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:03.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:03.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:04.002][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.004][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.007][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.016][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:04.018][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:04.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.021][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.023][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:04.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:04.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.031][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:04.032][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:04.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.035][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:04.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:04.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:04.054][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:04.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.059][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.061][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:04.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:04.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.068][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:04.069][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:04.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.073][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.096][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:04.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:04.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.107][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:04.109][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:04.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.113][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.119][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:04.121][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.125][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.127][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:04.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.134][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:04.136][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:04.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.139][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:04.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:04.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.151][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:04.153][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:04.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.156][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:04.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:04.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.164][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:04.166][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:04.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.178][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.180][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:04.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:04.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.196][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:04.198][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:04.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.201][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.213][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:04.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:04.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:04.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:04.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:04.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:04.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:04.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:04.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:04.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:04.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:04.392][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-05-03 20:27:04.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:04.516][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:04.531][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:04.542][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 20:27:04.553][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:04.556][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 20:27:04.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:04.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:04.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:04.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:04.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:04.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:04.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:04.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:04.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:04.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:04.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:04.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:04.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:04.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:04.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:04.794][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:04.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:04.805][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:04.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:04.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:04.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:04.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:04.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.857][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:04.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:04.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:04.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:04.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:04.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:04.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:04.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:04.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:04.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:04.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:04.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.159][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.310][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.389][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.538][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.650][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.692][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.703][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.758][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.762][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:05.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:05.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:05.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:05.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:05.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:05.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:05.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:05.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:05.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:05.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:05.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:06.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:06.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:06.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:06.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:06.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:06.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:06.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:06.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:06.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:06.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:06.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:06.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:06.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:06.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:06.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:06.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:06.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:06.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:06.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:06.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:06.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:06.147][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:06.153][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:06.155][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:06.158][private$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[2024-05-03 20:27:06.606][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[2024-05-03 20:27:07.039][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:07.050][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-05-03 20:27:07.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-05-03 20:27:07.061][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[2024-05-03 20:27:07.064][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:07.065][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:07.068][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-03 20:27:07.591][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-03 20:27:07.999][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:08.001][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-05-03 20:27:08.004][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-05-03 20:27:08.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:08.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:08.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:08.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:08.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:08.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:08.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:08.017][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-05-03 20:27:08.019][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:27:08.020][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-05-03 20:27:08.021][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:27:08.022][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:27:08.023][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:08.024][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:27:08.025][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:27:08.025][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:27:08.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:08.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:08.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:08.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:08.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:08.045][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:08.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:08.047][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-05-03 20:27:08.059][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:08.060][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:08.061][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-05-03 20:27:08.526][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-05-03 20:27:08.956][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:08.957][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-05-03 20:27:08.972][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-05-03 20:27:08.974][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-05-03 20:27:08.975][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:27:08.976][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:27:08.977][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:27:08.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:08.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:08.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:08.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:08.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:08.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:08.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:08.990][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:08.991][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:08.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:08.992][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:08.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:08.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:08.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:08.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:08.997][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:08.998][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:08.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:08.999][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.041][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:09.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:09.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.045][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:09.046][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:09.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.047][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.049][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:09.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:09.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:09.054][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:09.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.055][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:09.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:09.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.060][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:09.060][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:09.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.062][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.063][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:09.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:09.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.067][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:09.068][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:09.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.069][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.070][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:09.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:09.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.073][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:09.074][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:09.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.076][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.077][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:09.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:09.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.080][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.081][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.082][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.087][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:09.088][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:09.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.090][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:09.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:09.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.094][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:09.095][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:09.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.097][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.098][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:09.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:09.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.103][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:09.103][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:09.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.105][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.106][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:09.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:09.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:09.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:09.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:09.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:09.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:09.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:09.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:09.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:09.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:09.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:09.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:09.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:09.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:09.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:09.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:09.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:09.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:09.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:09.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:09.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:09.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:09.166][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-05-03 20:27:09.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:09.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:09.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:09.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:09.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:09.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:09.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:09.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:09.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:09.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:09.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:09.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:09.199][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:09.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:09.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:09.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:09.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:09.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:09.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:09.211][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-05-03 20:27:09.211][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:27:09.213][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-05-03 20:27:09.214][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:27:09.215][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:27:09.216][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:09.218][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:27:09.219][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:27:09.219][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:27:09.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:09.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:09.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:09.230][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:09.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:09.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:09.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:09.234][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-05-03 20:27:09.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:09.237][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:09.238][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-05-03 20:27:09.685][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-05-03 20:27:10.159][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:10.162][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-05-03 20:27:10.165][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-05-03 20:27:10.167][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-05-03 20:27:10.169][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:27:10.170][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:27:10.171][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:27:10.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.188][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.189][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.192][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.198][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:10.199][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:10.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.201][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.202][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:10.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:10.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.205][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:10.206][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:10.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.208][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.209][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:10.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:10.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.214][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:10.215][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:10.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.217][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.218][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:10.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:10.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.223][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:10.224][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:10.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.225][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:10.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:10.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.230][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:10.231][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:10.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.232][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.234][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:10.236][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:10.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.238][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.239][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:10.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:10.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.243][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.245][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.249][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:10.250][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:10.251][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.252][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:10.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:10.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.256][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:10.269][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:10.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.270][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.271][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:10.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:10.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.285][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:10.285][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:10.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.298][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:10.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:10.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:10.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:10.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:10.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:10.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:10.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:10.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:10.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:10.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.352][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-05-03 20:27:10.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.357][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.393][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:10.397][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:10.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 20:27:10.399][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:10.400][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 20:27:10.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.453][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.597][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.656][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:10.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:10.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:10.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:10.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:10.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:10.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:10.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:10.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:10.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:10.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:10.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:11.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:11.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:11.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:11.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:11.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:11.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:11.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:11.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:11.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:11.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:11.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:11.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:11.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:11.203][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:11.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:11.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:11.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:11.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:11.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:11.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:11.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:11.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:11.404][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:11.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:11.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:11.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:11.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:11.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:11.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:11.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:11.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:11.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:11.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:11.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:11.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:11.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:11.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:11.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:11.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:11.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.066][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:12.083][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:12.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-05-03 20:27:12.099][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:12.113][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-05-03 20:27:12.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.428][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.601][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.727][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.936][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:12.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:12.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:12.973][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:12.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:12.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:12.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:12.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:12.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:12.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:12.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:12.988][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:13.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:13.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:13.285][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.301][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.359][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:13.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:13.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:13.399][biodb::testThat]
biodb.INFO [2024-05-03 20:27:13.400][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-05-03 20:27:13.401][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:13.401][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:13.403][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 20:27:13.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 20:27:13.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:13.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:13.435][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:13.438][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:13.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-03 20:27:13.440][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:13.442][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-03 20:27:13.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.457][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:13.472][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:13.476][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:13.477][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-03 20:27:13.478][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:13.480][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-03 20:27:13.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:13.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:13.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:13.537][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:27:13.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.560][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.562][private$selectFields]
biodb.TRACE[2024-05-03 20:27:13.563][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:13.565][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:13.566][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.567][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.568][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.571][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.572][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.575][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.575][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.576][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.578][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.579][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.580][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:13.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.602][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-03 20:27:13.603][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.604][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.616][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.TRACE[2024-05-03 20:27:13.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.629][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.630][private$selectFields]
biodb.TRACE[2024-05-03 20:27:13.632][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:13.633][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:13.635][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.636][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.640][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.642][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.644][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.646][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.648][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.649][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.650][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.651][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.653][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.654][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:13.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.678][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 20:27:13.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:13.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.700][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.701][private$selectFields]
biodb.TRACE[2024-05-03 20:27:13.702][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:13.703][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:13.704][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.706][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.707][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.709][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.712][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.715][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.716][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.717][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:13.719][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.720][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.722][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.724][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:13.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:13.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.737][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-03 20:27:13.744][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:27:13.745][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:27:13.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:13.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:13.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:13.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:13.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:13.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:13.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:13.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:13.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:13.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:13.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:13.829][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:13.832][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:13.833][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:13.834][private$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[2024-05-03 20:27:14.288][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[2024-05-03 20:27:14.700][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:14.702][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-05-03 20:27:14.706][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-05-03 20:27:14.714][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[2024-05-03 20:27:14.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:14.720][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:14.722][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-05-03 20:27:15.194][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-05-03 20:27:15.709][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:15.711][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-05-03 20:27:15.716][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-05-03 20:27:15.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:15.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:15.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:15.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:15.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:15.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:15.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:15.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:15.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:15.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:15.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:15.756][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:15.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:15.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:15.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:15.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:15.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:15.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:15.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:15.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:15.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:15.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:15.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:15.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:15.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:15.837][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:27:15.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:15.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:15.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:15.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:15.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:15.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:15.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:15.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.924][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:15.925][private$selectFields]
biodb.TRACE[2024-05-03 20:27:15.925][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:15.926][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:15.927][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:15.928][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.929][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.930][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.931][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.933][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.937][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.938][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:15.939][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:15.940][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.942][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.943][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:15.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:15.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:15.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:15.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.008][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-03 20:27:16.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.091][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.092][private$selectFields]
biodb.TRACE[2024-05-03 20:27:16.092][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:16.093][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:16.094][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.095][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.098][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.098][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.099][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.101][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.122][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.123][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.124][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.125][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.126][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:16.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.137][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 20:27:16.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.156][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.157][private$selectFields]
biodb.TRACE[2024-05-03 20:27:16.158][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:16.158][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:16.159][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.160][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.161][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.162][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.163][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.164][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.178][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.179][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.181][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.182][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.183][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.185][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.185][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:16.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.198][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-03 20:27:16.199][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:27:16.201][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:27:16.209][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:16.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:16.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:16.217][biodb::testThat]
biodb.INFO [2024-05-03 20:27:16.218][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-05-03 20:27:16.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:16.220][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:16.223][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 20:27:16.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 20:27:16.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:16.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:16.278][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:16.298][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:16.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-03 20:27:16.300][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:16.312][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-03 20:27:16.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:16.358][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:16.361][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:16.362][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-03 20:27:16.363][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:16.364][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-03 20:27:16.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:16.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:16.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:16.410][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:27:16.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.450][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.453][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.454][private$selectFields]
biodb.TRACE[2024-05-03 20:27:16.455][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:16.456][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:16.457][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.458][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.472][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.474][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.475][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.477][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.478][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.479][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.485][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.486][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.487][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.488][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:16.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.499][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-03 20:27:16.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.515][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.516][private$selectFields]
biodb.TRACE[2024-05-03 20:27:16.517][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:16.518][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:16.519][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.520][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.521][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.522][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.523][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.524][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.525][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.526][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.527][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.528][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.529][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.531][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.531][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:16.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.543][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 20:27:16.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.562][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.562][private$selectFields]
biodb.TRACE[2024-05-03 20:27:16.563][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:16.564][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:16.565][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.566][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.566][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.568][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.569][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.572][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.573][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.574][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.575][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.575][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.577][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.578][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:16.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.589][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-03 20:27:16.590][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:27:16.591][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:27:16.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:16.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:16.647][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:16.649][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:16.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-03 20:27:16.652][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:16.653][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-03 20:27:16.655][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:16.657][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:16.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-03 20:27:16.661][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:16.662][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-03 20:27:16.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:16.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:16.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.747][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:16.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:16.763][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:27:16.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.793][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.794][private$selectFields]
biodb.TRACE[2024-05-03 20:27:16.806][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:16.808][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:16.819][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.820][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.821][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.823][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.824][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.825][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.826][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.827][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.828][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.840][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.841][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.853][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.854][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:16.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.866][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-03 20:27:16.867][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.884][private$selectFields]
biodb.TRACE[2024-05-03 20:27:16.885][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:16.885][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:16.886][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.888][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.889][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.891][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.891][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.892][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.894][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.895][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.895][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.896][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.897][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.900][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.901][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:16.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.916][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 20:27:16.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:16.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:16.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:16.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:16.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:16.927][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:16.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:16.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.938][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.939][private$selectFields]
biodb.TRACE[2024-05-03 20:27:16.940][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:16.941][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:16.942][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.943][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.943][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.946][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.947][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.949][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.950][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.951][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:16.952][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.953][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.954][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.955][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:16.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:16.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:16.967][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-03 20:27:16.968][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:27:16.969][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:27:16.977][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:16.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:16.988][biodb::testThat]
biodb.INFO [2024-05-03 20:27:16.989][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-05-03 20:27:16.990][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:16.991][biodb::testThat]
biodb.TRACE[2024-05-03 20:27:16.996][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-05-03 20:27:17.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-05-03 20:27:17.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:17.030][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:17.043][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:17.045][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:17.046][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-05-03 20:27:17.047][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:17.049][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-05-03 20:27:17.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:17.083][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:17.088][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:17.089][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-05-03 20:27:17.090][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:17.091][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-05-03 20:27:17.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:17.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:17.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:17.135][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:27:17.136][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.153][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.154][private$selectFields]
biodb.TRACE[2024-05-03 20:27:17.155][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:17.155][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:17.156][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.157][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.158][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.159][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.160][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.161][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.163][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.164][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.165][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.169][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.170][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:17.171][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.181][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-05-03 20:27:17.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.191][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[2024-05-03 20:27:17.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.196][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.200][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.201][private$selectFields]
biodb.TRACE[2024-05-03 20:27:17.201][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:17.202][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:17.203][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.204][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.205][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.206][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.207][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.208][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.210][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.222][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.224][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.226][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.228][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.229][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:17.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.240][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 20:27:17.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.270][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.271][private$selectFields]
biodb.TRACE[2024-05-03 20:27:17.272][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:17.273][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:17.273][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.274][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.275][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.276][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.277][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.278][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.279][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.285][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.286][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.287][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.288][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.289][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.290][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:17.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.300][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-05-03 20:27:17.301][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:27:17.301][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:27:17.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:17.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:17.348][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:17.351][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:17.352][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-05-03 20:27:17.353][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:17.355][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-05-03 20:27:17.357][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:27:17.360][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:27:17.361][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-05-03 20:27:17.362][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:27:17.364][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-05-03 20:27:17.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:17.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:17.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:17.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:17.427][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-05-03 20:27:17.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.446][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.447][private$selectFields]
biodb.TRACE[2024-05-03 20:27:17.448][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:17.449][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:17.450][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.450][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.451][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.453][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.454][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.455][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.457][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.457][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.458][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.459][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.460][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.461][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.462][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:17.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.473][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-05-03 20:27:17.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.484][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.492][private$selectFields]
biodb.TRACE[2024-05-03 20:27:17.493][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:17.493][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:17.494][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.495][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.497][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.498][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.499][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.501][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.502][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.503][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.506][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.507][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:17.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.529][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-05-03 20:27:17.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:17.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.548][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.549][private$selectFields]
biodb.TRACE[2024-05-03 20:27:17.550][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-05-03 20:27:17.551][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-05-03 20:27:17.552][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.552][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.553][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.555][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.557][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.557][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.559][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.560][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.561][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-05-03 20:27:17.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.562][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.564][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.565][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-05-03 20:27:17.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:17.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:17.601][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-05-03 20:27:17.602][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-05-03 20:27:17.603][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-05-03 20:27:17.634][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:17.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-05-03 20:27:17.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:17.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-05-03 20:27:17.641][biodb::testThat]
biodb.INFO [2024-05-03 20:27:17.648][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-05-03 20:27:17.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:17.650][biodb::testThat]
biodb.DEBUG[2024-05-03 20:27:17.651][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-05-03 20:27:17.652][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:27:17.653][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-05-03 20:27:17.654][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:27:17.656][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:27:17.657][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:17.657][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:27:17.659][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:27:17.659][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:27:17.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:17.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:17.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:17.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:17.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:17.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:17.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:17.672][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-05-03 20:27:17.674][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:17.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:17.676][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-05-03 20:27:18.224][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-05-03 20:27:18.714][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:27:18.716][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-05-03 20:27:18.720][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-05-03 20:27:18.722][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-05-03 20:27:18.724][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:27:18.725][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:27:18.726][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:27:18.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:18.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:18.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:18.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:18.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:18.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:18.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:27:18.739][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.740][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.741][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.745][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:27:18.746][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:27:18.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.748][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.749][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:27:18.750][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:27:18.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.752][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.753][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:27:18.754][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:27:18.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.755][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.756][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:27:18.757][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:27:18.758][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.759][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.760][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:18.761][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:27:18.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.762][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.763][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:27:18.764][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:27:18.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.766][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.767][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:18.768][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:27:18.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.769][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.770][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:27:18.771][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:27:18.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.773][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.774][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:27:18.775][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:27:18.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.776][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.777][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:27:18.778][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:27:18.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.780][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:18.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:18.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:18.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:18.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:27:18.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:27:18.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:27:18.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:27:18.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:27:18.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:27:18.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:27:18.816][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-05-03 20:27:18.817][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-05-03 20:27:18.826][biodb::testThat]
biodb.INFO [2024-05-03 20:27:18.827][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-05-03 20:27:18.828][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:27:18.828][biodb::testThat]
biodb.DEBUG[2024-05-03 20:27:18.838][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-05-03 20:27:18.839][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-05-03 20:27:18.840][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-05-03 20:27:18.841][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-05-03 20:27:18.843][cch$loadFileContent] file.exist = [3]: "FALSE, TRUE, FALSE".
biodb.TRACE[2024-05-03 20:27:18.844][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml".
biodb.DEBUG[2024-05-03 20:27:18.857][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:27:18.858][conn$getEntryContent] 2 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:27:18.859][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:27:18.860][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:27:18.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:27:18.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:27:18.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:27:18.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:27:18.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:27:18.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:27:18.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:27:18.886][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-05-03 20:27:18.889][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:27:18.890][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:27:18.891][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-05-03 20:27:23.943][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.INFO [2024-05-03 20:28:24.422][private$doSendRequestLoop] Error while retrieving HTTP header: simpleWarning in max(i): no non-missing arguments to max; returning -Inf
. When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB". Retrying connection to server...
biodb.DEBUG[2024-05-03 20:28:24.497][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:28:24.514][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:28:24.599][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-05-03 20:28:25.316][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-05-03 20:28:25.775][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:28:25.786][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-05-03 20:28:25.799][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-05-03 20:28:25.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:25.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:25.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:25.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:25.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:25.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:25.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:25.841][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-05-03 20:28:25.854][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:28:25.857][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:28:25.860][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-05-03 20:28:26.304][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-05-03 20:28:26.738][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:28:26.747][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-05-03 20:28:26.761][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-05-03 20:28:26.815][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-05-03 20:28:26.822][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:28:26.876][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-05-03 20:28:26.898][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-05-03 20:28:26.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:26.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:26.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:27.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:27.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:27.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:27.035][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[2024-05-03 20:28:27.118][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:27.127][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:27.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.131][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:27.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:27.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.156][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:28:27.158][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:28:27.160][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.162][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.173][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:27.176][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:27.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.180][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.184][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:28:27.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:28:27.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.190][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.192][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:28:27.194][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:28:27.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.198][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.201][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:27.203][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:27.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.207][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.210][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:28:27.212][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:28:27.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.216][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.220][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:27.222][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:27.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.225][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.227][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:27.241][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:27.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.257][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.261][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:28:27.263][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:28:27.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.268][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.275][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:28:27.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:28:27.282][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.284][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:27.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:27.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:27.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:27.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:27.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:27.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:27.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:27.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:27.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:27.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:27.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:27.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:27.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:27.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:27.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:27.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:27.435][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:27.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:27.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:28.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:28.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:28.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:28.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:28.484][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:28.488][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:28.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.493][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:28.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:28.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.509][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:28:28.513][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:28:28.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.546][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.557][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:28:28.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:28:28.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.575][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:28.579][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:28.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.671][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.841][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:28.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:28.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.923][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:28:28.927][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:28:28.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.932][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.938][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:28:28.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:28:28.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.951][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:28:28.956][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:28:28.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:28.965][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:28.981][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:28:28.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:28:29.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.035][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:29.045][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:29.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.062][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.089][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:29.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:29.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.221][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:28:29.247][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:28:29.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.328][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.349][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:28:29.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:28:29.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.442][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:29.461][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:29.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.484][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:29.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:29.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.513][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:29.530][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:29.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.601][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:29.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:29.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.650][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:28:29.674][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:28:29.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.708][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.720][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:28:29.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:28:29.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.743][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:28:29.811][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:28:29.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.884][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.896][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:28:29.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:28:29.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:29.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:29.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:29.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:29.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:29.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:29.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:30.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:30.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:30.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:30.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:30.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:30.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:30.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:30.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:30.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:30.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:30.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:30.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:30.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:30.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:30.651][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:30.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:30.807][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:30.815][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:30.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.818][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:30.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:30.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.913][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:28:30.916][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:28:30.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.927][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.929][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:28:30.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:28:30.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:30.950][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:30.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:30.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:30.977][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.018][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:31.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.057][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:28:31.058][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:28:31.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.060][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:28:31.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:28:31.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.087][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:28:31.095][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:28:31.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.147][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:28:31.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:28:31.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.185][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:31.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:31.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.212][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.223][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:31.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:31.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.278][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:28:31.283][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:28:31.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.286][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.296][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:28:31.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:28:31.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.301][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:31.303][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:31.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.305][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:31.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:31.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.328][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:31.330][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:31.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.333][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.347][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:31.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:31.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.353][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:28:31.354][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:28:31.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.357][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.359][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:28:31.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:28:31.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.362][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:28:31.363][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:28:31.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.368][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:28:31.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:28:31.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:31.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:31.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:31.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:31.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:31.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:31.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:31.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:31.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:31.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:31.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:31.515][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-05-03 20:28:31.516][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-05-03 20:28:31.518][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-05-03 20:28:31.589][biodb::testThat]
biodb.INFO [2024-05-03 20:28:31.597][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-05-03 20:28:31.600][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:31.602][biodb::testThat]
biodb.INFO [2024-05-03 20:28:31.803][biodb::testThat]
biodb.INFO [2024-05-03 20:28:31.811][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-05-03 20:28:31.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:31.813][biodb::testThat]
biodb.INFO [2024-05-03 20:28:31.824][biodb::testThat]
biodb.INFO [2024-05-03 20:28:31.825][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-05-03 20:28:31.826][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:31.827][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:31.830][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[2024-05-03 20:28:31.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:28:31.835][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:28:31.837][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-05-03 20:28:32.714][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-05-03 20:28:33.619][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:28:33.623][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-05-03 20:28:33.633][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-05-03 20:28:33.659][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:33.661][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:33.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:33.662][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:33.663][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:33.664][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:33.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:33.666][ef$get] fields variable is a list.
biodb.INFO [2024-05-03 20:28:33.667][biodb::testThat]
biodb.INFO [2024-05-03 20:28:33.668][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-05-03 20:28:33.669][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:33.671][biodb::testThat]
biodb.ERROR[2024-05-03 20:28:33.719][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-05-03 20:28:33.819][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-05-03 20:28:33.844][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 20:28:33.847][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-03 20:28:33.851][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-03 20:28:33.852][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 20:28:33.854][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:33.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:33.857][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:33.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:33.860][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 20:28:33.896][biodb::testContext]
biodb.INFO [2024-05-03 20:28:33.897][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:33.899][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-05-03 20:28:33.900][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:33.902][biodb::testContext]
biodb.INFO [2024-05-03 20:28:33.910][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:33.912][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:33.921][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:33.923][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 20:28:33.925][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 20:28:33.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.929][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 20:28:33.931][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 20:28:33.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.935][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 20:28:33.936][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 20:28:33.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.941][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 20:28:33.942][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 20:28:33.943][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 20:28:33.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.947][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 20:28:33.948][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 20:28:33.950][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 20:28:33.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.953][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 20:28:33.954][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 20:28:33.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.959][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 20:28:33.960][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 20:28:33.961][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 20:28:33.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.965][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 20:28:33.966][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 20:28:33.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.970][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 20:28:33.972][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 20:28:33.973][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 20:28:33.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.978][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:33.979][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 20:28:33.980][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 20:28:33.982][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 20:28:33.983][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 20:28:33.984][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 20:28:33.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.989][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 20:28:33.990][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 20:28:33.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:33.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:33.996][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 20:28:33.997][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 20:28:33.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:33.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.004][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 20:28:34.005][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 20:28:34.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.010][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 20:28:34.011][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 20:28:34.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.017][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 20:28:34.019][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 20:28:34.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.025][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:34.026][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 20:28:34.071][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 20:28:34.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.076][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 20:28:34.077][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 20:28:34.078][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 20:28:34.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.088][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 20:28:34.095][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.103][self$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[2024-05-03 20:28:34.105][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.108][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:34.109][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.110][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.111][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.112][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.114][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:34.115][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:34.117][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.117][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 20:28:34.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:34.119][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.121][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.122][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:34.122][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:34.122][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:34.122][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:34.122][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:34.122][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:34.124][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.126][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:34.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.129][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.130][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.132][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:34.134][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:34.135][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.136][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.138][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 20:28:34.141][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.142][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:34.144][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.145][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:34.146][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.147][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.148][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.149][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.150][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:34.151][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:34.153][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.154][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 20:28:34.155][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:34.157][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.158][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.158][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:34.158][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:34.158][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:34.158][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:34.158][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:34.160][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:34.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.162][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:34.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.167][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:34.171][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:34.172][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.174][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.177][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 20:28:34.179][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.181][self$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[2024-05-03 20:28:34.182][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.183][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:34.184][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.186][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.187][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.188][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.189][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:34.190][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:34.191][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.193][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 20:28:34.194][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:34.195][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.195][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.196][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.197][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:34.199][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.200][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:34.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.202][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.204][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.206][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.207][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:34.208][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:34.209][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.211][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.212][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 20:28:34.213][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.217][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:34.218][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.219][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:34.220][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.221][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.222][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.223][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.225][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:34.226][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:34.228][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.231][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 20:28:34.232][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:34.233][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.234][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.236][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.237][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:34.238][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.239][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.241][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:34.242][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.243][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.244][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.245][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.247][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:34.259][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:34.261][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.262][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:34.265][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:34.266][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.309][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[2024-05-03 20:28:34.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.314][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[2024-05-03 20:28:34.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.354][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 20:28:34.358][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 20:28:34.362][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 20:28:34.364][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 20:28:34.366][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:28:34.367][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 20:28:34.369][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:34.370][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:34.372][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 20:28:34.374][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 20:28:34.375][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:28:34.376][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 20:28:34.378][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:34.379][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:34.381][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 20:28:34.382][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:28:34.384][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 20:28:34.386][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 20:28:34.387][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:28:34.390][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 20:28:34.392][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 20:28:34.394][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 20:28:34.395][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 20:28:34.397][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 20:28:34.398][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 20:28:34.400][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 20:28:34.402][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 20:28:34.404][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 20:28:34.405][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 20:28:34.408][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 20:28:34.410][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 20:28:34.412][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 20:28:34.414][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 20:28:34.416][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 20:28:34.418][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 20:28:34.422][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 20:28:34.424][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 20:28:34.426][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 20:28:34.428][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 20:28:34.430][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 20:28:34.432][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 20:28:34.435][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 20:28:34.436][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 20:28:34.438][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 20:28:34.440][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 20:28:34.442][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 20:28:34.444][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 20:28:34.446][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 20:28:34.448][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 20:28:34.450][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 20:28:34.453][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 20:28:34.455][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 20:28:34.457][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 20:28:34.459][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 20:28:34.461][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 20:28:34.463][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 20:28:34.465][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 20:28:34.467][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 20:28:34.469][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 20:28:34.470][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 20:28:34.472][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 20:28:34.474][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 20:28:34.476][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 20:28:34.478][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 20:28:34.480][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 20:28:34.482][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 20:28:34.487][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:28:34.490][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:28:34.491][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 20:28:34.493][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 20:28:34.495][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 20:28:34.497][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 20:28:34.499][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 20:28:34.502][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 20:28:34.504][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 20:28:34.506][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 20:28:34.508][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 20:28:34.510][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 20:28:34.512][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 20:28:34.514][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 20:28:34.516][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 20:28:34.518][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 20:28:34.519][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 20:28:34.523][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 20:28:34.525][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:34.533][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:34.535][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.538][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.562][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[2024-05-03 20:28:34.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.573][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.577][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[2024-05-03 20:28:34.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.584][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[2024-05-03 20:28:34.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.601][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[2024-05-03 20:28:34.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.666][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[2024-05-03 20:28:34.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:34.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.694][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:34.698][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-03 20:28:34.701][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.702][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.704][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.705][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:34.726][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.737][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.740][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.741][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-03 20:28:34.743][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-03 20:28:34.744][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:34.745][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.747][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-03 20:28:34.748][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-03 20:28:34.750][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-03 20:28:34.751][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:34.753][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:34.753][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:34.753][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:34.754][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-03 20:28:34.756][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.759][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:34.760][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:34.761][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:34.762][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:34.764][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:28:34.764][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-03 20:28:34.765][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:34.766][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:34.767][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:34.768][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-03 20:28:34.768][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-03 20:28:34.771][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:28:34.774][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:28:34.776][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-03 20:28:34.777][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:28:34.778][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:28:34.780][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:28:34.795][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-03 20:28:34.797][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-03 20:28:34.801][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-03 20:28:34.805][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-03 20:28:34.807][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 20:28:34.810][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 20:28:34.813][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-03 20:28:34.816][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-03 20:28:34.821][biodb::testThat]
biodb.INFO [2024-05-03 20:28:34.823][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-05-03 20:28:34.824][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:34.826][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:34.841][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-03 20:28:34.851][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:34.853][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-03 20:28:34.855][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:34.858][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-03 20:28:34.861][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:34.864][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:34.867][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-03 20:28:34.869][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:34.872][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-03 20:28:34.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:34.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.894][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:34.898][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:34.900][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-03 20:28:34.902][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:34.904][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-03 20:28:34.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:34.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.948][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:34.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.971][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:34.975][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:34.977][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-03 20:28:34.979][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:34.980][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-03 20:28:34.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:34.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:34.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:34.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:34.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:34.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:34.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:34.999][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:35.003][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:35.005][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-03 20:28:35.007][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:35.010][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-03 20:28:35.014][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:35.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:35.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:35.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:35.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:35.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:35.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:35.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:35.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:35.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:35.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:35.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:35.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:35.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:35.054][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:35.058][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:35.060][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-05-03 20:28:35.062][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:35.065][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-05-03 20:28:35.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:35.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:35.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:35.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:35.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:35.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:35.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:35.086][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:35.093][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:35.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-05-03 20:28:35.098][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:35.100][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-05-03 20:28:35.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:35.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:35.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:35.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:35.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:35.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:35.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:35.121][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:35.124][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:35.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70e3912746e7e39b39fbbffe6c90b502".
biodb.TRACE[2024-05-03 20:28:35.128][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:35.133][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content".
biodb.DEBUG[2024-05-03 20:28:35.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:35.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:35.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:35.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:35.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:35.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:35.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 20:28:35.165][biodb::testThat]
biodb.INFO [2024-05-03 20:28:35.166][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-05-03 20:28:35.167][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:35.168][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:35.172][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:35.177][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:28:35.179][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:28:35.183][private$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[2024-05-03 20:28:35.665][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[2024-05-03 20:28:36.093][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:28:36.096][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-05-03 20:28:36.103][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-05-03 20:28:36.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:36.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:36.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:36.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:36.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:36.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:36.122][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[2024-05-03 20:28:36.128][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[2024-05-03 20:28:36.158][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:28:36.160][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:28:36.162][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-05-03 20:28:36.905][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-05-03 20:28:37.332][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:28:37.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-05-03 20:28:37.337][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-05-03 20:28:37.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:37.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 20:28:37.361][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 20:28:37.362][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-03 20:28:37.363][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-03 20:28:37.364][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 20:28:37.365][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.367][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.370][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 20:28:37.392][biodb::testContext]
biodb.INFO [2024-05-03 20:28:37.403][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:37.404][biodb::testContext] Test context - Test web services
biodb.INFO [2024-05-03 20:28:37.404][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:37.405][biodb::testContext]
biodb.INFO [2024-05-03 20:28:37.407][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:37.410][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:37.417][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:37.418][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 20:28:37.419][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 20:28:37.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.422][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 20:28:37.423][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 20:28:37.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.426][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 20:28:37.427][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 20:28:37.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.429][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[2024-05-03 20:28:37.430][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 20:28:37.431][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 20:28:37.431][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 20:28:37.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.434][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 20:28:37.436][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 20:28:37.437][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 20:28:37.438][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.439][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[2024-05-03 20:28:37.440][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 20:28:37.441][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 20:28:37.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.444][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 20:28:37.445][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 20:28:37.446][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 20:28:37.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.448][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[2024-05-03 20:28:37.449][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 20:28:37.450][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 20:28:37.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.454][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 20:28:37.455][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 20:28:37.455][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 20:28:37.456][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.458][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:37.459][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 20:28:37.460][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 20:28:37.461][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 20:28:37.462][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 20:28:37.463][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 20:28:37.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.468][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 20:28:37.469][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 20:28:37.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.472][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.DEBUG[2024-05-03 20:28:37.484][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 20:28:37.485][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 20:28:37.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.488][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 20:28:37.489][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 20:28:37.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.492][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 20:28:37.493][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 20:28:37.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.496][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 20:28:37.497][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 20:28:37.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.499][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:37.501][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 20:28:37.529][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 20:28:37.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.533][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 20:28:37.534][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 20:28:37.535][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 20:28:37.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.538][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 20:28:37.539][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.540][self$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[2024-05-03 20:28:37.541][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.542][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:37.543][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.544][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.545][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.546][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.547][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:37.548][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:37.549][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.550][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 20:28:37.551][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:37.552][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.552][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.553][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:37.553][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:37.553][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:37.553][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:37.553][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:37.554][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:37.555][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:37.555][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:37.556][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:37.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:37.558][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:37.559][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.560][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.561][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:37.561][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:37.562][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.563][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.564][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 20:28:37.565][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.566][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:37.567][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.568][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:37.570][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.571][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.572][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.573][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.574][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:37.575][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:37.575][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.576][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 20:28:37.577][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:37.578][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.579][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:37.579][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:37.579][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:37.579][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:37.579][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:37.580][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:37.582][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:37.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:37.594][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:37.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:37.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:37.597][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.598][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.599][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:37.610][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:37.611][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.612][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.613][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 20:28:37.614][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.615][self$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[2024-05-03 20:28:37.616][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.617][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:37.618][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.618][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.619][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.620][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.632][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:37.634][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:37.636][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.637][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 20:28:37.638][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:37.640][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.641][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.642][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.643][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:37.644][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:37.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:37.645][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:37.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:37.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:37.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.648][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.649][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:37.650][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:37.651][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.652][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.654][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 20:28:37.666][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.668][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:37.669][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.670][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:37.671][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.672][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.673][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.674][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.675][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:37.676][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:37.677][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.677][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 20:28:37.678][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:37.679][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.680][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:37.681][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.682][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:37.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:37.684][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:37.685][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:37.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:37.686][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:37.687][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:37.688][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.689][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:37.690][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:37.690][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:37.691][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:37.692][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:37.693][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.738][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[2024-05-03 20:28:37.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.743][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[2024-05-03 20:28:37.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.789][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[2024-05-03 20:28:37.790][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 20:28:37.792][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 20:28:37.794][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 20:28:37.796][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 20:28:37.797][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:28:37.798][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 20:28:37.799][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:37.801][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:37.802][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 20:28:37.803][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 20:28:37.804][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:28:37.805][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 20:28:37.807][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:37.808][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:37.809][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 20:28:37.810][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:28:37.811][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 20:28:37.813][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 20:28:37.820][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:28:37.821][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 20:28:37.822][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 20:28:37.823][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 20:28:37.825][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 20:28:37.826][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 20:28:37.827][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 20:28:37.828][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 20:28:37.830][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 20:28:37.831][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 20:28:37.832][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 20:28:37.833][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 20:28:37.834][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 20:28:37.835][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 20:28:37.836][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 20:28:37.837][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 20:28:37.838][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 20:28:37.839][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 20:28:37.840][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 20:28:37.841][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 20:28:37.843][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 20:28:37.845][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 20:28:37.846][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 20:28:37.847][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 20:28:37.849][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 20:28:37.850][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 20:28:37.852][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 20:28:37.853][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 20:28:37.854][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 20:28:37.855][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 20:28:37.856][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 20:28:37.857][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 20:28:37.859][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 20:28:37.860][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 20:28:37.861][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 20:28:37.862][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 20:28:37.862][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 20:28:37.863][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 20:28:37.865][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 20:28:37.866][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 20:28:37.867][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 20:28:37.868][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 20:28:37.870][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 20:28:37.871][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 20:28:37.872][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 20:28:37.873][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 20:28:37.874][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 20:28:37.875][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 20:28:37.876][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:28:37.877][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:28:37.879][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 20:28:37.880][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 20:28:37.881][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 20:28:37.882][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 20:28:37.883][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 20:28:37.884][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 20:28:37.885][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 20:28:37.887][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 20:28:37.888][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 20:28:37.889][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 20:28:37.890][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 20:28:37.891][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 20:28:37.893][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 20:28:37.894][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 20:28:37.895][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 20:28:37.896][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 20:28:37.898][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:37.899][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:37.900][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.901][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.942][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[2024-05-03 20:28:37.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.948][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[2024-05-03 20:28:37.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.967][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[2024-05-03 20:28:37.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:37.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:37.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:37.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:37.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:37.985][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[2024-05-03 20:28:37.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:37.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:37.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:38.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:38.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:38.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:38.004][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[2024-05-03 20:28:38.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:38.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:38.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:38.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:38.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:38.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:38.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:38.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:38.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:38.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:38.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:38.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:38.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:38.017][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[2024-05-03 20:28:38.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:38.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:38.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:38.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:38.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:38.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:38.023][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[2024-05-03 20:28:38.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:38.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:38.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:38.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:38.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:38.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:38.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:38.033][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:38.034][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-03 20:28:38.036][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:38.038][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 20:28:38.039][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:38.040][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:38.042][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:38.043][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:38.044][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:38.045][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-03 20:28:38.046][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-03 20:28:38.046][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:38.047][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:38.048][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-03 20:28:38.049][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-03 20:28:38.050][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-03 20:28:38.051][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:38.052][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:38.052][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:38.052][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:38.053][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-03 20:28:38.054][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:38.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:38.058][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:38.059][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:38.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:38.061][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:38.062][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:28:38.062][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-03 20:28:38.063][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:38.064][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:38.065][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:38.065][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-03 20:28:38.065][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-03 20:28:38.067][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:28:38.068][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:28:38.070][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-03 20:28:38.072][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:28:38.074][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:28:38.076][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:28:38.079][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-03 20:28:38.080][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-03 20:28:38.081][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-03 20:28:38.083][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-03 20:28:38.085][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 20:28:38.086][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 20:28:38.087][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-03 20:28:38.088][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-03 20:28:38.089][biodb::testThat]
biodb.INFO [2024-05-03 20:28:38.090][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-05-03 20:28:38.091][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:38.092][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:38.095][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-03 20:28:38.098][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:38.101][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-03 20:28:38.104][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:38.106][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-03 20:28:38.111][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-05-03 20:28:38.114][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:28:38.115][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:28:38.116][private$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[2024-05-03 20:28:41.186][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[2024-05-03 20:28:41.652][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:28:41.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-05-03 20:28:41.658][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-05-03 20:28:41.691][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 20:28:41.693][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-03 20:28:41.705][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-03 20:28:41.706][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 20:28:41.707][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:41.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:41.709][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:41.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:41.711][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-05-03 20:28:41.716][biodb::testContext]
biodb.INFO [2024-05-03 20:28:41.717][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:41.719][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-05-03 20:28:41.720][biodb::testContext] ********************************************************************************
biodb.INFO [2024-05-03 20:28:41.720][biodb::testContext]
biodb.INFO [2024-05-03 20:28:41.724][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:41.752][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:41.757][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:41.758][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-05-03 20:28:41.759][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-05-03 20:28:41.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.773][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-05-03 20:28:41.774][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-05-03 20:28:41.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.777][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-05-03 20:28:41.778][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-05-03 20:28:41.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.781][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-05-03 20:28:41.782][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-05-03 20:28:41.784][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-05-03 20:28:41.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.787][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-05-03 20:28:41.788][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-05-03 20:28:41.788][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-05-03 20:28:41.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.791][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-05-03 20:28:41.792][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-05-03 20:28:41.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.796][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-05-03 20:28:41.797][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-05-03 20:28:41.798][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-05-03 20:28:41.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.801][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-05-03 20:28:41.802][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-05-03 20:28:41.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.806][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-05-03 20:28:41.806][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-05-03 20:28:41.807][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-05-03 20:28:41.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.810][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:41.811][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-05-03 20:28:41.812][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-05-03 20:28:41.813][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-05-03 20:28:41.813][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-05-03 20:28:41.814][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-05-03 20:28:41.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.818][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-05-03 20:28:41.830][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-05-03 20:28:41.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.833][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-05-03 20:28:41.834][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-05-03 20:28:41.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.836][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[2024-05-03 20:28:41.837][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-05-03 20:28:41.838][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-05-03 20:28:41.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.841][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-05-03 20:28:41.842][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-05-03 20:28:41.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.845][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-05-03 20:28:41.846][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-05-03 20:28:41.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.849][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-05-03 20:28:41.850][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-05-03 20:28:41.947][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-05-03 20:28:41.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.951][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-05-03 20:28:41.952][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-05-03 20:28:41.953][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-05-03 20:28:41.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:41.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:41.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:41.957][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-05-03 20:28:41.958][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:41.959][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-05-03 20:28:41.960][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:41.961][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:41.961][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:41.962][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:41.963][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:41.965][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:41.966][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:41.967][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:41.968][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:41.969][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-05-03 20:28:41.969][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:41.970][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:41.971][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:41.972][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:41.972][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:41.972][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:41.972][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:41.972][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:41.972][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:41.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:41.974][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:41.975][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:41.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:41.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:41.977][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:41.979][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:41.980][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:41.980][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:41.981][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:41.982][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:41.983][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-05-03 20:28:41.984][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:41.985][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:41.986][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:41.987][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:41.989][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:41.990][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:41.991][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:41.991][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:41.992][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:41.993][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:41.994][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:41.995][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-05-03 20:28:41.996][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:41.996][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:41.997][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:41.998][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:41.998][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:41.998][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:41.998][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-05-03 20:28:41.998][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-05-03 20:28:42.000][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:42.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:42.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:42.003][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:42.004][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:42.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:42.005][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.006][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.006][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:42.007][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:42.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.009][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.010][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-05-03 20:28:42.012][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.024][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-05-03 20:28:42.025][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.025][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:42.026][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.027][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.028][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.028][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.029][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-05-03 20:28:42.030][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:42.031][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.031][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-05-03 20:28:42.032][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:42.033][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.035][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.036][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.037][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:42.038][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:42.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:42.039][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:42.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:42.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:42.042][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.042][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.043][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:42.044][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:42.044][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.045][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.046][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-05-03 20:28:42.048][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.049][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-05-03 20:28:42.050][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.051][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:42.052][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.052][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.053][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.054][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.055][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-05-03 20:28:42.055][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:42.056][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.057][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-05-03 20:28:42.058][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:42.059][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.060][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.071][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.072][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-05-03 20:28:42.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:42.074][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:42.074][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:42.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:42.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:42.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.078][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.078][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:42.079][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:42.080][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.081][self$setPropertyValue]
biodb.DEBUG[2024-05-03 20:28:42.083][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:42.084][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.084][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[2024-05-03 20:28:42.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.114][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[2024-05-03 20:28:42.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.126][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[2024-05-03 20:28:42.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.155][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[2024-05-03 20:28:42.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.159][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[2024-05-03 20:28:42.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.174][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-05-03 20:28:42.175][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-05-03 20:28:42.176][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-05-03 20:28:42.177][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-05-03 20:28:42.179][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:28:42.180][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-05-03 20:28:42.181][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:42.182][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:42.183][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-05-03 20:28:42.185][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-05-03 20:28:42.187][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:28:42.189][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-05-03 20:28:42.201][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-05-03 20:28:42.224][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-05-03 20:28:42.225][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-05-03 20:28:42.226][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-05-03 20:28:42.228][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-05-03 20:28:42.229][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-05-03 20:28:42.230][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:28:42.231][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-05-03 20:28:42.232][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-05-03 20:28:42.233][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-05-03 20:28:42.235][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-05-03 20:28:42.236][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-05-03 20:28:42.237][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-05-03 20:28:42.239][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-05-03 20:28:42.244][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-05-03 20:28:42.245][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-05-03 20:28:42.247][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-05-03 20:28:42.248][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-05-03 20:28:42.249][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-05-03 20:28:42.250][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-05-03 20:28:42.251][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-05-03 20:28:42.252][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-05-03 20:28:42.253][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-05-03 20:28:42.254][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-05-03 20:28:42.256][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-05-03 20:28:42.257][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-05-03 20:28:42.258][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-05-03 20:28:42.259][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-05-03 20:28:42.260][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-05-03 20:28:42.261][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-05-03 20:28:42.262][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-05-03 20:28:42.263][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-05-03 20:28:42.264][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-05-03 20:28:42.265][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-05-03 20:28:42.266][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-05-03 20:28:42.268][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-05-03 20:28:42.269][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-05-03 20:28:42.270][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-05-03 20:28:42.272][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-05-03 20:28:42.273][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-05-03 20:28:42.274][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-05-03 20:28:42.275][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-05-03 20:28:42.276][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-05-03 20:28:42.277][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-05-03 20:28:42.278][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-05-03 20:28:42.280][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-05-03 20:28:42.281][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-05-03 20:28:42.282][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-05-03 20:28:42.283][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-05-03 20:28:42.284][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-05-03 20:28:42.285][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-05-03 20:28:42.286][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-05-03 20:28:42.287][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-05-03 20:28:42.289][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-05-03 20:28:42.290][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:28:42.291][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:28:42.292][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-05-03 20:28:42.293][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-05-03 20:28:42.294][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-05-03 20:28:42.295][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-05-03 20:28:42.296][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-05-03 20:28:42.297][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-05-03 20:28:42.298][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-05-03 20:28:42.300][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-05-03 20:28:42.301][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-05-03 20:28:42.302][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-05-03 20:28:42.303][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-05-03 20:28:42.304][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-05-03 20:28:42.305][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-05-03 20:28:42.306][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-05-03 20:28:42.307][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-05-03 20:28:42.308][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-05-03 20:28:42.310][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-05-03 20:28:42.311][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-05-03 20:28:42.312][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.314][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.314][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[2024-05-03 20:28:42.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.330][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[2024-05-03 20:28:42.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.378][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[2024-05-03 20:28:42.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.384][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[2024-05-03 20:28:42.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.389][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[2024-05-03 20:28:42.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.395][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[2024-05-03 20:28:42.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.400][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[2024-05-03 20:28:42.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.405][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[2024-05-03 20:28:42.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-05-03 20:28:42.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.416][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[2024-05-03 20:28:42.419][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-05-03 20:28:42.420][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-05-03 20:28:42.422][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.440][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.441][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.442][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-05-03 20:28:42.443][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.444][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.445][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.446][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-05-03 20:28:42.447][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-05-03 20:28:42.448][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-05-03 20:28:42.449][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.450][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-05-03 20:28:42.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-05-03 20:28:42.452][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-05-03 20:28:42.453][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-05-03 20:28:42.454][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-05-03 20:28:42.454][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-05-03 20:28:42.454][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-05-03 20:28:42.455][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-05-03 20:28:42.456][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:42.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:42.457][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-05-03 20:28:42.458][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-05-03 20:28:42.459][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-05-03 20:28:42.460][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-05-03 20:28:42.460][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:28:42.460][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-05-03 20:28:42.461][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-05-03 20:28:42.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-05-03 20:28:42.462][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-05-03 20:28:42.464][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-05-03 20:28:42.464][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-05-03 20:28:42.476][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-05-03 20:28:42.478][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-05-03 20:28:42.479][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-05-03 20:28:42.480][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-05-03 20:28:42.481][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-05-03 20:28:42.483][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-05-03 20:28:42.485][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-05-03 20:28:42.486][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-05-03 20:28:42.488][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-05-03 20:28:42.489][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-05-03 20:28:42.490][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 20:28:42.491][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-05-03 20:28:42.492][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-05-03 20:28:42.493][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-05-03 20:28:42.494][biodb::testThat]
biodb.INFO [2024-05-03 20:28:42.495][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-05-03 20:28:42.495][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-05-03 20:28:42.496][biodb::testThat]
biodb.DEBUG[2024-05-03 20:28:42.499][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-05-03 20:28:42.502][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:42.503][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-05-03 20:28:42.504][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:42.505][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-05-03 20:28:42.509][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[2024-05-03 20:28:42.512][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-05-03 20:28:42.513][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-05-03 20:28:42.514][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-05-03 20:28:42.515][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-05-03 20:28:42.528][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-05-03 20:28:42.529][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-05-03 20:28:42.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-05-03 20:28:42.532][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-05-03 20:28:42.533][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-05-03 20:28:42.534][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-05-03 20:28:42.535][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-05-03 20:28:42.535][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-05-03 20:28:42.536][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-05-03 20:28:42.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:42.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:42.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:42.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:42.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:42.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:42.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-05-03 20:28:42.548][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-05-03 20:28:42.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-05-03 20:28:42.551][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-05-03 20:28:42.552][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-05-03 20:28:43.776][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-05-03 20:28:45.145][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-05-03 20:28:45.147][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-05-03 20:28:45.164][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-05-03 20:28:45.167][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-05-03 20:28:45.169][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-05-03 20:28:45.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-05-03 20:28:45.172][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-05-03 20:28:45.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-05-03 20:28:45.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:45.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:45.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:45.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:45.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:45.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-05-03 20:28:45.335][ef$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.336][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.338][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.343][ef$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:28:45.343][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:28:45.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.345][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.390][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-05-03 20:28:45.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-05-03 20:28:45.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.394][ef$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:45.395][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:45.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.397][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.399][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-05-03 20:28:45.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-05-03 20:28:45.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.402][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-05-03 20:28:45.403][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-05-03 20:28:45.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.405][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.406][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-05-03 20:28:45.408][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-05-03 20:28:45.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.410][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.411][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:45.412][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:45.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.414][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.415][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:45.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-05-03 20:28:45.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.419][ef$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:28:45.420][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:28:45.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.422][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.423][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-05-03 20:28:45.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-05-03 20:28:45.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.427][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:45.428][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:45.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.429][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:45.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-05-03 20:28:45.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.436][ef$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:45.437][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:45.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.440][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.455][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-05-03 20:28:45.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-05-03 20:28:45.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.458][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:28:45.459][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:28:45.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.461][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.462][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-05-03 20:28:45.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-05-03 20:28:45.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.466][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:28:45.467][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:28:45.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.468][ef$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.470][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-05-03 20:28:45.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-05-03 20:28:45.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:45.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:45.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:45.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:45.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-05-03 20:28:45.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-05-03 20:28:45.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-05-03 20:28:45.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-05-03 20:28:45.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-05-03 20:28:45.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-05-03 20:28:45.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-05-03 20:28:45.533][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-05-03 20:28:45.536][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-05-03 20:28:45.537][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-05-03 20:28:45.538][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-05-03 20:28:45.539][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-05-03 20:28:45.540][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-05-03 20:28:45.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-05-03 20:28:45.542][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-05-03 20:28:45.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-05-03 20:28:45.543][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-05-03 20:28:45.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 385 ]
> 
> proc.time()
   user  system elapsed 
 23.476   2.176 143.635 

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.6420.9944.917
ChebiEntry0.4670.0190.499