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This page was generated on 2024-06-07 11:37:52 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 200/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: RELEASE_3_19
git_last_commit: fad38a4
git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for biodbChebi on nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.10.0.tar.gz
StartedAt: 2024-06-05 20:59:58 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 21:01:52 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 114.2 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbChebi_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-06-05 21:00:42.657][biodb::testContext]
biodb.INFO [2024-06-05 21:00:42.660][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-05 21:00:42.661][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-06-05 21:00:42.662][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-05 21:00:42.663][biodb::testContext]
biodb.INFO [2024-06-05 21:00:42.671][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-05 21:00:42.673][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-05 21:00:42.682][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:00:42.683][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-05 21:00:42.684][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-05 21:00:42.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.688][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-05 21:00:42.710][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-05 21:00:42.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.714][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.DEBUG[2024-06-05 21:00:42.715][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-05 21:00:42.716][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-05 21:00:42.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.720][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-05 21:00:42.721][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-05 21:00:42.722][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-05 21:00:42.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.726][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-05 21:00:42.727][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-05 21:00:42.728][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-05 21:00:42.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.732][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-05 21:00:42.733][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-05 21:00:42.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.737][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-05 21:00:42.738][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-05 21:00:42.739][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-05 21:00:42.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.744][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-05 21:00:42.745][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-05 21:00:42.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.749][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-05 21:00:42.750][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-05 21:00:42.751][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-05 21:00:42.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.755][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-05 21:00:42.757][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-05 21:00:42.758][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-05 21:00:42.759][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-05 21:00:42.760][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-05 21:00:42.761][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-05 21:00:42.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.765][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-05 21:00:42.766][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-05 21:00:42.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.770][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-05 21:00:42.772][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-05 21:00:42.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.776][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-05 21:00:42.777][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-05 21:00:42.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.781][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-05 21:00:42.782][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-05 21:00:42.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.785][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[2024-06-05 21:00:42.786][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-05 21:00:42.788][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-05 21:00:42.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.792][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-05 21:00:42.793][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-05 21:00:42.798][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-05 21:00:42.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.802][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-05 21:00:42.803][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-05 21:00:42.804][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-05 21:00:42.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:42.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:42.812][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-05 21:00:42.853][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.884][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-05 21:00:42.885][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.886][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:00:42.887][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.888][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.889][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.891][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.892][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-05 21:00:42.893][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:00:42.894][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.895][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-05 21:00:42.896][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:00:42.897][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.898][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.899][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:00:42.899][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:00:42.899][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:00:42.899][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-05 21:00:42.899][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-05 21:00:42.900][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:00:42.901][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:42.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:42.903][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:00:42.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:42.905][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:42.906][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.907][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.908][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:00:42.909][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:00:42.910][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.911][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.913][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-05 21:00:42.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.916][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-05 21:00:42.917][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.918][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:00:42.919][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.920][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.920][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.921][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.922][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-05 21:00:42.923][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:00:42.924][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.925][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-05 21:00:42.926][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:00:42.927][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.928][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.929][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:00:42.929][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:00:42.929][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:00:42.929][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-05 21:00:42.929][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-05 21:00:42.930][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:00:42.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:42.932][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:42.932][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:00:42.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:42.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:42.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.936][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.937][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:00:42.938][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:00:42.939][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.939][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.941][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-05 21:00:42.942][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.943][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-05 21:00:42.944][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.945][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:00:42.946][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.948][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.949][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.950][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-05 21:00:42.951][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:00:42.952][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.952][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-05 21:00:42.953][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:00:42.954][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.955][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.956][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.957][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:00:42.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:42.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:42.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:00:42.961][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:42.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:42.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.963][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.964][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:00:42.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:00:42.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.967][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.968][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-05 21:00:42.969][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.970][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-05 21:00:42.971][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:00:42.973][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.974][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.975][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.976][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.977][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-05 21:00:42.978][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:00:42.979][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.980][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-05 21:00:42.980][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:00:42.981][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.982][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:42.983][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.984][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:00:42.985][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:42.986][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:42.987][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:00:42.988][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:42.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:42.989][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:00:42.990][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.991][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:00:42.992][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:00:42.993][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:42.994][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:00:42.998][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:00:42.999][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:42.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.035][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[2024-06-05 21:00:43.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.048][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[2024-06-05 21:00:43.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.071][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[2024-06-05 21:00:43.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.077][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-05 21:00:43.082][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-05 21:00:43.084][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-05 21:00:43.085][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-05 21:00:43.087][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-05 21:00:43.088][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-05 21:00:43.090][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-05 21:00:43.091][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-05 21:00:43.093][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-05 21:00:43.094][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-05 21:00:43.096][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-05 21:00:43.098][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-05 21:00:43.099][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-05 21:00:43.101][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-05 21:00:43.102][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-05 21:00:43.104][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-05 21:00:43.106][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-05 21:00:43.107][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-05 21:00:43.108][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-05 21:00:43.110][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-05 21:00:43.112][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-05 21:00:43.113][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-05 21:00:43.115][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-05 21:00:43.116][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-05 21:00:43.118][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-05 21:00:43.119][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-05 21:00:43.121][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-05 21:00:43.122][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-05 21:00:43.124][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-05 21:00:43.125][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-05 21:00:43.126][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-05 21:00:43.128][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-05 21:00:43.129][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-05 21:00:43.130][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-05 21:00:43.132][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-05 21:00:43.141][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-05 21:00:43.142][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-05 21:00:43.144][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-05 21:00:43.145][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-05 21:00:43.146][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-05 21:00:43.148][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-05 21:00:43.149][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-05 21:00:43.151][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-05 21:00:43.152][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-05 21:00:43.154][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-05 21:00:43.155][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-05 21:00:43.157][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-05 21:00:43.158][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-05 21:00:43.160][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-05 21:00:43.161][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-05 21:00:43.162][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-05 21:00:43.164][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-05 21:00:43.165][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-05 21:00:43.167][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-05 21:00:43.168][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-05 21:00:43.170][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-05 21:00:43.171][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-05 21:00:43.173][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-05 21:00:43.174][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-05 21:00:43.176][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-05 21:00:43.177][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-05 21:00:43.178][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-05 21:00:43.180][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-05 21:00:43.181][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-05 21:00:43.182][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-05 21:00:43.184][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-05 21:00:43.185][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-05 21:00:43.186][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-05 21:00:43.188][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-05 21:00:43.189][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-05 21:00:43.190][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-05 21:00:43.192][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-05 21:00:43.193][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-05 21:00:43.194][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-05 21:00:43.196][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-05 21:00:43.197][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-05 21:00:43.198][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-05 21:00:43.199][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-05 21:00:43.201][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-05 21:00:43.202][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-05 21:00:43.203][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-05 21:00:43.205][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-05 21:00:43.206][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-05 21:00:43.212][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-05 21:00:43.213][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-05 21:00:43.217][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:00:43.217][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.219][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.220][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[2024-06-05 21:00:43.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.282][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[2024-06-05 21:00:43.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.288][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[2024-06-05 21:00:43.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.294][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[2024-06-05 21:00:43.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.300][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[2024-06-05 21:00:43.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.313][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[2024-06-05 21:00:43.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:00:43.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:43.328][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-05 21:00:43.339][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-05 21:00:43.342][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:43.343][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-05 21:00:43.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:43.345][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:00:43.346][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:43.347][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:00:43.348][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:43.349][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-05 21:00:43.350][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-05 21:00:43.351][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:00:43.352][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:43.353][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-05 21:00:43.354][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-05 21:00:43.355][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-05 21:00:43.357][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-05 21:00:43.358][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:00:43.358][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:00:43.358][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:00:43.359][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-05 21:00:43.360][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:43.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:43.361][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:00:43.362][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:00:43.363][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:00:43.364][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:00:43.365][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:43.365][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-05 21:00:43.366][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:00:43.367][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:00:43.368][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-05 21:00:43.369][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-05 21:00:43.369][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-05 21:00:43.376][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-05 21:00:43.378][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-05 21:00:43.380][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-05 21:00:43.381][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-05 21:00:43.383][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-05 21:00:43.384][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-05 21:00:43.420][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-05 21:00:43.421][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-05 21:00:43.426][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-05 21:00:43.431][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-05 21:00:43.436][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-05 21:00:43.437][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-05 21:00:43.438][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-05 21:00:43.439][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-05 21:00:43.450][biodb::testThat]
biodb.INFO [2024-06-05 21:00:43.451][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-06-05 21:00:43.452][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:43.454][biodb::testThat]
biodb.TRACE[2024-06-05 21:00:43.458][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-06-05 21:00:43.460][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:43.464][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:43.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:43.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:43.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:43.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:43.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:43.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:43.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:43.504][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.505][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.507][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.525][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:43.526][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:43.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.528][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.555][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:43.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:43.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.559][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:43.560][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:43.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.562][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.564][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:43.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:43.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.568][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:43.569][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:43.570][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.571][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:43.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:43.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.577][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:43.578][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:43.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.580][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:43.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:43.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.586][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:43.587][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:43.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.589][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.591][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:43.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:43.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.595][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:43.596][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:43.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.598][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.600][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:43.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:43.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.604][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:43.606][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:43.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.608][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:43.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:43.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.614][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:43.615][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:43.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.617][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:43.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:43.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.623][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:43.624][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:43.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.626][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.628][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:43.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:43.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.632][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:43.633][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:43.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.635][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.637][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:43.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:43.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.650][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:43.740][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-06-05 21:00:43.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:43.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:43.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:43.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:43.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.773][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:43.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:43.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:43.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:43.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:43.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:43.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:43.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:43.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.790][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-05 21:00:43.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-05 21:00:43.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-05 21:00:43.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-05 21:00:43.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.798][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-05 21:00:43.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-05 21:00:43.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-05 21:00:43.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-05 21:00:43.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.921][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.922][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.923][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.924][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:43.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:43.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.993][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.995][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:43.997][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:43.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:43.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:44.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.024][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.025][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.039][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:44.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:44.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:44.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:44.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:44.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:44.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.051][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:44.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:44.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.054][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:44.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:44.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.071][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.079][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.080][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.082][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.108][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.109][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.125][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:44.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:44.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.129][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:44.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:44.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.134][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:44.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:44.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.138][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:44.139][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:44.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.141][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.142][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:44.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:44.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.156][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.161][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.170][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.171][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.173][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.174][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.187][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.192][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.197][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.201][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.202][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.205][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.206][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.220][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:44.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:44.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.226][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:44.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:44.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.241][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:44.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:44.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.245][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:44.247][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:44.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.249][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.250][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:44.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:44.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.275][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.276][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.278][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.291][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:44.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:44.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.295][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:44.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:44.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:44.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:44.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.302][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:44.303][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:44.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.305][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.306][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:44.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:44.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.318][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.319][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.321][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.325][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:44.326][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:44.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.328][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.333][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:44.334][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:44.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.336][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.341][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:44.342][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:44.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.344][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.348][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.349][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.351][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.355][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.356][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.358][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.363][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.364][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.366][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.370][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.372][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.374][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.378][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.379][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.382][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.387][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.388][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.390][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.394][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:44.396][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:44.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.397][ef$get] fields variable is a list.
biodb.INFO [2024-06-05 21:00:44.405][biodb::testThat]
biodb.INFO [2024-06-05 21:00:44.407][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-05 21:00:44.408][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:44.409][biodb::testThat]
biodb.DEBUG[2024-06-05 21:00:44.423][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-06-05 21:00:44.432][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:44.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-06-05 21:00:44.439][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:44.440][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-06-05 21:00:44.442][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:44.467][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:44.468][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:44.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:44.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:44.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:44.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:44.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:44.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:44.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:44.492][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.493][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.495][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.518][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:44.520][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:44.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.522][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.523][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:44.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:44.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.527][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:44.528][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:44.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.530][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:44.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:44.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.535][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:44.536][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:44.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.538][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:44.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:44.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.543][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.544][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.546][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:44.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.551][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.552][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.553][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.555][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:44.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.559][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:44.560][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.561][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.563][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:44.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.567][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.569][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.574][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.575][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.577][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.579][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.583][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:44.583][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.585][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.587][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:44.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:44.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.591][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:44.592][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:44.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.594][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.595][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:44.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:44.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:44.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:44.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:44.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:44.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:44.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:44.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:44.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:44.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:44.643][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-06-05 21:00:44.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-05 21:00:44.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-05 21:00:44.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-05 21:00:44.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-05 21:00:44.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-05 21:00:44.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-05 21:00:44.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-05 21:00:44.664][biodb::testThat]
biodb.INFO [2024-06-05 21:00:44.666][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-05 21:00:44.667][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:44.668][biodb::testThat]
biodb.TRACE[2024-06-05 21:00:44.671][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.672][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.674][ef$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:44.676][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-06-05 21:00:44.712][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.721][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:44.728][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-06-05 21:00:44.734][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-05 21:00:44.754][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:00:44.770][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-05 21:00:44.772][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:44.774][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-05 21:00:44.798][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:00:44.803][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:00:44.805][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-05 21:00:44.806][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:44.808][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-05 21:00:44.810][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-06-05 21:00:44.823][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.825][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:44.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.827][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.828][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:44.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.831][ef$get] fields variable is a list.
biodb.INFO [2024-06-05 21:00:44.836][biodb::testThat]
biodb.INFO [2024-06-05 21:00:44.837][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-06-05 21:00:44.838][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:44.839][biodb::testThat]
biodb.TRACE[2024-06-05 21:00:44.865][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:44.875][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:44.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:44.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:44.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:44.953][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:00:44.957][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:00:44.959][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-05 21:00:44.960][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:44.962][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-06-05 21:00:44.979][biodb::testThat]
biodb.INFO [2024-06-05 21:00:44.980][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-06-05 21:00:44.981][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:44.982][biodb::testThat]
biodb.TRACE[2024-06-05 21:00:45.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:45.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:45.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:45.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:45.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:45.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:45.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:45.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:45.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:45.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:45.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:45.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:45.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-05 21:00:45.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-05 21:00:45.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.029][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-05 21:00:45.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-05 21:00:45.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.033][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-05 21:00:45.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-05 21:00:45.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.036][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-05 21:00:45.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-05 21:00:45.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:45.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:45.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:45.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:45.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:45.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:45.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:45.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:45.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:45.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:45.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:45.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:45.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.086][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-05 21:00:45.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-05 21:00:45.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.090][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-05 21:00:45.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-05 21:00:45.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.094][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-05 21:00:45.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-05 21:00:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:45.099][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-05 21:00:45.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-05 21:00:45.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:45.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-05 21:00:45.110][biodb::testThat]
biodb.INFO [2024-06-05 21:00:45.111][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-05 21:00:45.112][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:45.113][biodb::testThat]
biodb.INFO [2024-06-05 21:00:45.123][biodb::testThat]
biodb.INFO [2024-06-05 21:00:45.124][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-05 21:00:45.125][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:45.126][biodb::testThat]
biodb.INFO [2024-06-05 21:00:45.134][biodb::testThat]
biodb.INFO [2024-06-05 21:00:45.135][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-05 21:00:45.136][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:45.137][biodb::testThat]
biodb.DEBUG[2024-06-05 21:00:45.141][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-06-05 21:00:45.831][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-06-05 21:00:47.263][biodb::testThat]
biodb.INFO [2024-06-05 21:00:47.264][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-05 21:00:47.265][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:47.267][biodb::testThat]
biodb.DEBUG[2024-06-05 21:00:47.703][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-06-05 21:00:48.142][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:48.143][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:48.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.146][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:48.147][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:48.148][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:48.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.150][ef$get] fields variable is a list.
biodb.INFO [2024-06-05 21:00:48.153][biodb::testThat]
biodb.INFO [2024-06-05 21:00:48.154][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-06-05 21:00:48.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:00:48.156][biodb::testThat]
biodb.TRACE[2024-06-05 21:00:48.167][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:48.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:48.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:48.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:48.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:48.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:48.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:48.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:48.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:48.276][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:00:48.279][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:00:48.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-05 21:00:48.282][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:48.284][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-05 21:00:48.342][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:00:48.345][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:00:48.347][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-05 21:00:48.348][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:48.349][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-06-05 21:00:48.362][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-05 21:00:48.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-05 21:00:48.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:48.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:48.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:48.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:48.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:48.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:48.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:48.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:48.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:00:48.398][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:00:48.400][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-05 21:00:48.401][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:48.402][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-05 21:00:48.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:48.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:48.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:48.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:48.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:48.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:48.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:48.415][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-06-05 21:00:48.467][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:48.469][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-06-05 21:00:48.470][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:48.471][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:48.472][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:48.473][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:48.474][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:48.475][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:48.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:48.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:48.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:48.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:48.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:48.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:48.487][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[2024-06-05 21:00:48.488][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-06-05 21:00:48.491][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:48.492][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:48.493][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-06-05 21:00:49.165][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-06-05 21:00:49.585][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:49.587][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-06-05 21:00:49.602][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-06-05 21:00:49.604][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-06-05 21:00:49.606][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:49.607][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:49.608][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:49.610][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:49.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:49.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:49.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:49.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:49.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:49.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:49.621][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.622][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.624][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.629][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:49.630][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:49.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.632][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.633][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:49.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:49.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.637][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:49.638][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:49.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.640][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.641][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:49.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:49.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.645][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:49.646][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:49.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.648][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:49.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:49.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.653][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:49.654][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:49.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.655][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:49.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:49.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.660][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:49.661][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:49.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.663][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.664][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:49.665][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.667][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.668][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:49.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.680][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:49.681][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:49.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.683][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:49.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:49.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.687][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:49.689][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:49.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.690][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.692][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:49.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:49.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.696][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:49.697][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:49.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.699][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.700][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:49.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:49.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.704][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:49.705][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:49.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.707][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.708][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:49.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:49.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:49.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:49.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:49.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:49.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:49.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:49.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:49.753][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-06-05 21:00:49.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:49.775][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:00:49.778][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:00:49.779][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-05 21:00:49.780][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:49.782][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-05 21:00:49.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:49.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:49.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:49.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:49.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:49.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:49.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:49.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:49.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:49.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:49.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:49.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:49.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:49.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:49.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:49.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:49.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:49.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:49.843][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-06-05 21:00:49.845][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:49.847][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-06-05 21:00:49.848][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:49.849][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:49.850][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:49.852][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:49.853][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:49.854][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:49.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:49.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:49.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:49.895][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:49.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:49.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:49.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:49.900][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-06-05 21:00:49.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:49.923][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:49.943][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-06-05 21:00:50.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-06-05 21:00:50.757][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:50.763][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-06-05 21:00:50.773][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-06-05 21:00:50.780][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-06-05 21:00:50.784][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:50.787][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:50.791][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:50.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:50.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:50.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:50.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:50.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:50.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:50.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:50.820][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.822][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.825][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.833][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:50.835][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:50.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.837][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.839][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:50.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:50.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.843][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:50.845][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:50.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.847][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.848][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:50.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:50.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.853][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:50.854][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:50.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:50.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:50.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.861][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:50.862][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:50.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.864][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:50.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:50.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.869][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:50.870][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:50.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.872][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.873][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:50.874][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:50.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.876][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.877][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:50.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:50.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.881][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:50.882][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:50.883][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.884][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:50.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:50.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.889][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:50.890][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:50.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.892][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:50.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:50.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.897][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:50.898][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:50.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.900][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.901][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:50.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:50.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.905][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:50.906][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:50.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.908][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.909][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:50.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:50.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:50.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:50.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:50.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:50.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:50.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:50.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:50.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:50.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:50.960][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-06-05 21:00:50.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:50.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:50.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:50.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:50.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:50.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:50.989][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:00:50.992][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:00:50.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-05 21:00:50.995][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:00:50.996][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-05 21:00:51.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:51.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:51.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:51.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:51.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:51.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:51.008][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[2024-06-05 21:00:51.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:51.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:51.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:51.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:51.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:51.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:51.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:51.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:51.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:51.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:51.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:51.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:51.028][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:51.029][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[2024-06-05 21:00:51.030][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-06-05 21:00:51.031][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:51.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-06-05 21:00:51.034][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:51.035][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:51.036][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:51.037][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:51.038][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:51.039][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:51.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:51.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:51.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:51.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:51.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:51.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:51.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:51.051][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-06-05 21:00:51.054][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:51.055][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:51.056][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-06-05 21:00:51.464][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-06-05 21:00:51.898][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:51.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-06-05 21:00:51.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-06-05 21:00:51.906][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-06-05 21:00:51.907][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:51.908][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:51.909][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:51.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:51.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:51.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:51.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:51.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:51.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:51.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:51.922][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:51.923][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:51.924][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.925][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:51.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:51.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.930][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:51.939][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:51.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.941][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.942][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:51.943][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:51.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.945][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.946][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:51.948][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:51.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.949][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.951][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:51.952][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:51.953][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.954][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.955][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:51.956][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:51.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.958][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.959][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:51.960][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:51.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.962][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.963][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:51.964][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:51.965][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.966][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.967][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:51.968][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:51.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.970][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:51.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:51.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.975][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:51.976][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:51.977][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.978][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.979][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:51.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:51.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:51.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:51.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.986][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:51.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:51.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:51.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:51.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:51.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:51.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:51.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:51.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:51.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:52.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:52.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:52.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:52.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:52.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:52.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:52.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:52.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:52.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:52.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:52.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:52.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:52.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:52.025][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-06-05 21:00:52.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:52.046][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:52.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:52.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:52.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:52.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:52.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:52.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:52.056][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-06-05 21:00:52.057][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:52.058][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-06-05 21:00:52.060][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:52.061][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:52.062][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:52.063][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:52.064][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:52.065][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:52.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:52.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:52.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:52.073][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:52.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:52.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:52.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:52.077][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-06-05 21:00:52.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:52.081][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:52.082][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-06-05 21:00:52.497][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-06-05 21:00:52.910][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:52.912][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-06-05 21:00:52.916][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-06-05 21:00:52.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-06-05 21:00:52.920][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:52.921][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:52.922][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:52.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:52.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:52.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:52.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:52.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:52.932][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:52.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:52.944][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:52.945][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:52.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.947][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:52.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:52.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.952][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:52.953][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:52.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.956][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.957][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:52.958][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:52.959][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.960][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.962][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:52.963][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:52.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.965][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.966][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:52.967][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:52.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.969][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.970][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:52.971][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:52.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.973][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.974][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:52.975][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:52.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.978][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:52.979][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:52.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.981][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.982][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:52.983][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:52.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:52.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:52.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.991][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:52.992][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:52.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.994][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.995][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:52.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:52.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:52.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:52.999][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:53.000][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:53.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.002][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:53.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:53.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:53.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:53.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:53.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:53.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:53.042][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-06-05 21:00:53.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.047][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:53.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:53.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:53.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:53.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:53.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:53.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:53.071][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:53.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:53.073][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-06-05 21:00:53.074][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:53.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-06-05 21:00:53.077][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:53.078][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:53.080][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:53.081][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:53.082][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:53.083][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:53.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:53.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:53.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:53.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:53.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:53.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:53.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:53.095][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-06-05 21:00:53.098][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:53.099][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:53.101][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-06-05 21:00:53.507][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-06-05 21:00:53.940][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:53.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-06-05 21:00:53.946][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-06-05 21:00:53.948][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-06-05 21:00:53.950][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:53.951][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:53.952][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:53.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:53.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:53.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:53.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:53.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:53.971][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:53.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:53.974][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.975][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.977][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:53.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:53.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.983][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:53.984][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:53.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.985][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.987][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:53.988][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:53.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.990][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.991][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:53.992][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:53.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.994][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.995][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:53.996][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:53.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:53.998][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:53.999][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:54.000][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:54.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.002][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.003][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:54.004][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.006][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.007][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:54.008][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:54.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.011][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:54.012][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:54.013][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.014][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.015][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:54.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:54.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.019][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:54.020][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:54.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.022][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.023][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:54.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:54.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.027][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:54.028][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:54.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.029][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:54.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:54.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:54.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:54.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:54.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:54.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:54.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:54.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:54.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:54.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:54.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:54.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:54.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:54.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:54.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:54.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:54.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:54.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:54.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:54.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:54.067][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-06-05 21:00:54.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:54.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:54.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:54.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:54.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:54.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:54.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:54.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:54.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:54.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:54.095][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[2024-06-05 21:00:54.097][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-06-05 21:00:54.097][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:54.099][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-06-05 21:00:54.100][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:54.101][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:54.102][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:54.103][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:54.104][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:54.105][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:54.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:54.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:54.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:54.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:54.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:54.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:54.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:54.117][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-06-05 21:00:54.120][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:54.121][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:54.122][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-06-05 21:00:54.533][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-06-05 21:00:54.958][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:54.976][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-06-05 21:00:54.983][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-06-05 21:00:54.990][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-06-05 21:00:54.993][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:54.996][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:54.999][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:55.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:55.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:55.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:55.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:55.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:55.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:55.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:55.021][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.023][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.033][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:55.034][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:55.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.037][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.038][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:55.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:55.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.043][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:55.044][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:55.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.046][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:55.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:55.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.052][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:55.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:55.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.055][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.057][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:55.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:55.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.061][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:55.062][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:55.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.064][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:55.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:55.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.069][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:55.070][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:55.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.072][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.073][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:55.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:55.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.077][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:55.078][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:55.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.080][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.081][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:55.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:55.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.085][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:55.086][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:55.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.088][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:55.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:55.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.093][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:55.094][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:55.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.096][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.097][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:55.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.101][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:55.102][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:55.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.104][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.106][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:55.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:55.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.110][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:55.111][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:55.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.113][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.114][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:55.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:55.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:55.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:55.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:55.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:55.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:55.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:55.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:55.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:55.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:55.156][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-06-05 21:00:55.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:55.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:55.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:55.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:55.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:55.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:55.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:55.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:55.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:55.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:55.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:55.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:55.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:55.183][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-06-05 21:00:55.184][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:55.185][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-06-05 21:00:55.187][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:55.188][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:55.189][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:55.190][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:55.191][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:55.192][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:55.194][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:55.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:55.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:55.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:55.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:55.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:55.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:55.204][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-06-05 21:00:55.207][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:55.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:55.209][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-06-05 21:00:55.612][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-06-05 21:00:56.024][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:56.028][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-06-05 21:00:56.035][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-06-05 21:00:56.041][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-06-05 21:00:56.044][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:56.047][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:56.049][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:56.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:56.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:56.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:56.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:56.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:56.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:56.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:56.076][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.077][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.080][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.088][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:56.090][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:56.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.092][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.094][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:56.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:56.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.099][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:56.100][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:56.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.102][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.104][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:56.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:56.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.108][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:56.109][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:56.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.111][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.113][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:56.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:56.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.116][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:56.117][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:56.118][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.119][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:56.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:56.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.124][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:56.125][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:56.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.127][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.128][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:56.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:56.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.132][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:56.133][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:56.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.135][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.136][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:56.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:56.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.140][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:56.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:56.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.142][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:56.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:56.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.147][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:56.148][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:56.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.150][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:56.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:56.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.155][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:56.156][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:56.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.158][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.159][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:56.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:56.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.163][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:56.164][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:56.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.165][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.167][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:56.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:56.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:56.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:56.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:56.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:56.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:56.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:56.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:56.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:56.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:56.216][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-06-05 21:00:56.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:56.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:56.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:56.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:56.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:56.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:56.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:56.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:56.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:56.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:56.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:56.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:56.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:56.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:56.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:56.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:56.238][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-06-05 21:00:56.238][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:56.240][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-06-05 21:00:56.241][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:56.242][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:56.243][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:56.244][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:56.245][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:56.246][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:56.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:56.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:56.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:56.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:56.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:56.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:56.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:56.258][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-06-05 21:00:56.261][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:56.262][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:56.263][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-06-05 21:00:56.662][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-06-05 21:00:57.062][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:57.064][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-06-05 21:00:57.067][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-06-05 21:00:57.070][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-06-05 21:00:57.071][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:57.072][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:57.073][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:57.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:57.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:57.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:57.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:57.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:57.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:57.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:57.085][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.086][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.087][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.092][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:57.093][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:57.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.095][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.096][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:57.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:57.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.100][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:57.101][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:57.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.103][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.104][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:57.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:57.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.107][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:57.108][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:57.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.110][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:57.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:57.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.115][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:57.116][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:57.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.118][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:57.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:57.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.123][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:57.124][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:57.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.125][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.126][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:57.127][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:57.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.129][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.130][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:57.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:57.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.134][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:57.135][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:57.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.137][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:57.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:57.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.142][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:57.143][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:57.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.145][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:57.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:57.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.150][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:57.151][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:57.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.152][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.153][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:57.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:57.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.162][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:57.166][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:57.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.167][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.169][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:57.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:57.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:57.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:57.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:57.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:57.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:57.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:57.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:57.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:57.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:57.210][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-06-05 21:00:57.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:57.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:57.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:57.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:57.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:57.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:57.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:57.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:57.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:57.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:57.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:57.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:57.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:57.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:57.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:57.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:57.231][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-06-05 21:00:57.232][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:57.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-06-05 21:00:57.235][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:57.236][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:57.237][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:57.238][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:57.239][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:57.240][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:57.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:57.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:57.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:57.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:57.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:57.250][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:57.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:57.252][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-06-05 21:00:57.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:57.255][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:57.257][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-06-05 21:00:57.666][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-06-05 21:00:58.073][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:58.075][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-06-05 21:00:58.078][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-06-05 21:00:58.081][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-06-05 21:00:58.082][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:58.083][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:58.085][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:58.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:58.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:58.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:58.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:58.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:58.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:58.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:58.097][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.098][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.100][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.105][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:58.106][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:58.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.108][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.110][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:58.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:58.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.114][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:58.115][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:58.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.116][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:58.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:58.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.122][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:58.123][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:58.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.125][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:58.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:58.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.130][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:58.131][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:58.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.133][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:58.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:58.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.138][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:58.139][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:58.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.141][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.142][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:58.143][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:58.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.154][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.156][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:58.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:58.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.160][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:58.161][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:58.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.163][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:58.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:58.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.168][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:58.169][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:58.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.171][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:58.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:58.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.176][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:58.177][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:58.178][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.179][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.180][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:58.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:58.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.184][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:58.185][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:58.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.187][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.188][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:58.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:58.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:58.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:58.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:58.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:58.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:58.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:58.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:58.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:58.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:58.229][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-06-05 21:00:58.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:58.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:58.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:58.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:58.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:58.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:58.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:58.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:58.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:58.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:58.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:58.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:58.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:58.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:58.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:58.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:58.250][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-06-05 21:00:58.251][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:58.253][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-06-05 21:00:58.254][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:58.255][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:58.256][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:58.257][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:58.258][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:58.259][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:58.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:58.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:58.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:58.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:58.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:58.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:58.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:58.271][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-06-05 21:00:58.274][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:58.275][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:58.276][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-06-05 21:00:58.678][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-06-05 21:00:59.116][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:00:59.118][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-06-05 21:00:59.121][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-06-05 21:00:59.124][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-06-05 21:00:59.125][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:00:59.127][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:00:59.128][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:00:59.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:59.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:59.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:59.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:59.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:59.138][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:59.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:00:59.141][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.142][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.143][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.144][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.149][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:59.150][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:59.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.152][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.154][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:00:59.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:00:59.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.165][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:59.166][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:59.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.168][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.169][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:00:59.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:00:59.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.173][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:59.174][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:59.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.176][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:00:59.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:00:59.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.181][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:59.182][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:59.183][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.183][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.185][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:00:59.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:00:59.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.188][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:59.189][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:00:59.190][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.191][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.192][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:59.193][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:59.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.195][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.196][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:00:59.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:59.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.200][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:59.201][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:59.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.203][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:59.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:00:59.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.208][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:59.209][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:59.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.212][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:00:59.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:00:59.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.215][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:59.216][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:59.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.218][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.219][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:00:59.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:00:59.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.223][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:59.224][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:59.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.226][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.227][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:00:59.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:00:59.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:59.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:59.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:59.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:59.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:00:59.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:00:59.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:00:59.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:00:59.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:59.267][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-06-05 21:00:59.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:59.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:59.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:59.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:59.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:00:59.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:59.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:00:59.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:00:59.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:00:59.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:59.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:59.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:59.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:59.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:59.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:59.288][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[2024-06-05 21:00:59.289][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-06-05 21:00:59.290][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:00:59.292][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-06-05 21:00:59.293][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:00:59.294][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:00:59.295][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:00:59.296][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:00:59.297][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:00:59.298][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:00:59.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:00:59.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:00:59.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:00:59.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:00:59.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:00:59.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:00:59.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:00:59.310][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-06-05 21:00:59.313][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:00:59.314][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:00:59.315][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-06-05 21:00:59.718][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-06-05 21:01:00.124][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:00.129][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-06-05 21:01:00.136][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-06-05 21:01:00.155][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-06-05 21:01:00.158][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:01:00.161][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:00.163][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:00.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:00.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:00.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:00.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:00.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:00.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:00.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:00.185][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.187][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.190][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.196][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:00.198][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:00.199][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.200][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.201][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:00.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:00.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.206][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:00.207][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:00.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.209][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.210][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:00.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:00.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.214][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:00.216][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:00.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.217][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:00.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:00.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.223][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:00.224][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:00.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.225][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:00.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:00.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.230][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:00.231][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:00.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.233][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.234][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:00.235][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:00.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.237][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.238][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:00.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:00.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.242][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:00.243][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:00.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.245][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:00.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:00.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.250][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:00.251][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:00.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.252][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.254][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:00.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:00.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.258][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:00.259][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:00.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.260][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.261][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:00.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:00.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.265][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:00.266][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:00.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.268][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.269][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:00.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:00.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:00.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:00.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:00.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:00.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:00.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:00.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:00.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:00.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:00.310][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-06-05 21:01:00.311][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:00.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:00.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:00.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:00.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:00.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:00.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:00.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:00.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:00.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:00.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:00.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:00.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:00.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:00.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:00.331][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[2024-06-05 21:01:00.332][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-06-05 21:01:00.333][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:00.335][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-06-05 21:01:00.368][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:01:00.370][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:01:00.371][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:00.372][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:01:00.374][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:01:00.374][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:01:00.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:00.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:00.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:00.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:00.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:00.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:00.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:00.387][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-06-05 21:01:00.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:00.391][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:00.392][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-06-05 21:01:00.800][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-06-05 21:01:01.253][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:01.257][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-06-05 21:01:01.262][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-06-05 21:01:01.267][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-06-05 21:01:01.270][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:01:01.272][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:01.274][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:01.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:01.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:01.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:01.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:01.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:01.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:01.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:01.296][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.298][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.301][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.309][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:01.310][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:01.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.313][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.315][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:01.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:01.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.319][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:01.321][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:01.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.323][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.324][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:01.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:01.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.329][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:01.330][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:01.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.332][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:01.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:01.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.337][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:01.338][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:01.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.340][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:01.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:01.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.345][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:01.346][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:01.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.348][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.349][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:01.350][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.352][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.353][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:01.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.357][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.358][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.359][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.364][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:01.365][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:01.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.367][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.369][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:01.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:01.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.372][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:01.373][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:01.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.375][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.376][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:01.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:01.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.380][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:01.381][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:01.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.383][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.384][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:01.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:01.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:01.459][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-06-05 21:01:01.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:01.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:01.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:01.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:01.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:01.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:01.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:01.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:01.485][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-06-05 21:01:01.486][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:01.489][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-06-05 21:01:01.491][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:01.492][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml".
biodb.DEBUG[2024-06-05 21:01:01.493][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:01.495][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:01.496][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:01.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:01.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:01.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:01.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:01.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:01.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:01.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:01.510][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.511][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.513][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.518][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:01.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:01.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.521][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.523][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:01.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:01.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.527][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:01.528][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:01.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.530][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:01.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.535][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:01.537][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:01.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.539][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.540][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:01.541][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:01.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.543][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.544][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:01.545][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:01.546][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.547][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.549][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:01.550][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.552][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.553][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:01.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.557][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.558][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.560][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.565][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:01.567][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:01.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.568][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:01.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:01.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.574][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:01.575][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:01.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.577][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.578][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:01.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:01.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.583][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:01.584][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:01.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.586][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:01.627][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-06-05 21:01:01.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:01.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:01.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:01.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:01.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:01.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:01.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:01.662][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[2024-06-05 21:01:01.664][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-06-05 21:01:01.666][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:01.669][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-06-05 21:01:01.671][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:01.675][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml".
biodb.DEBUG[2024-06-05 21:01:01.677][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:01.680][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:01.682][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:01.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:01.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:01.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:01.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:01.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:01.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:01.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:01.706][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.708][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.712][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.721][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:01.723][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:01.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.727][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.730][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:01.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:01.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.739][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:01.742][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:01.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.746][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:01.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:01.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.756][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:01.758][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:01.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.761][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.762][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:01.764][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:01.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.767][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.769][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:01.770][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:01.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.773][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.775][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:01.777][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.780][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.781][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:01.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.787][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.789][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.792][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:01.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.801][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:01.802][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:01.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.805][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.808][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:01.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:01.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.814][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:01.816][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:01.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.818][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.820][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:01.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:01.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.826][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:01.828][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:01.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.830][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:01.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:01.893][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-06-05 21:01:01.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:01.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:01.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:01.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:01.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:01.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:01.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:01.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:01.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:01.928][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-06-05 21:01:01.929][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:01.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-06-05 21:01:01.941][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:01.944][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml".
biodb.DEBUG[2024-06-05 21:01:01.946][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:01.947][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:01.949][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:01.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:01.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:01.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:01.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:01.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:01.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:01.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:01.968][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.970][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.972][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:01.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:01.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:01.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:01.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.004][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.006][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.009][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.011][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.017][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.018][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.021][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.022][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.028][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.030][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.033][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.040][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.042][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.045][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.047][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.053][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.054][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.058][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.059][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.061][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.064][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.066][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.072][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.074][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.077][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.085][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.086][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.090][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.097][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.099][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.103][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.109][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.111][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.113][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.115][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.180][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-06-05 21:01:02.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:02.215][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-06-05 21:01:02.217][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:02.220][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-06-05 21:01:02.222][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:02.229][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml".
biodb.DEBUG[2024-06-05 21:01:02.241][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:02.244][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:02.245][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:02.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:02.264][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.265][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.268][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.277][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.278][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.282][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.284][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.291][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.293][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.298][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.305][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.307][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.311][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.313][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.321][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.323][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.326][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.328][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.337][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.340][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.342][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.344][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.347][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.350][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.355][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.356][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.359][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.365][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.366][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.369][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.370][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.375][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.377][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.379][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.386][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.387][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.389][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.391][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.447][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-06-05 21:01:02.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:02.471][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-06-05 21:01:02.472][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:02.474][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-06-05 21:01:02.475][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:02.477][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml".
biodb.DEBUG[2024-06-05 21:01:02.479][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:02.480][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:02.489][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:02.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:02.502][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.504][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.505][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.511][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.512][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.513][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.515][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.519][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.520][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.522][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.527][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.528][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.530][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.535][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.536][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.538][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.543][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.544][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.546][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.547][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.548][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.550][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.551][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.555][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.556][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.558][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.563][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.564][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.566][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.567][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.571][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.572][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.574][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.575][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.579][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.580][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.582][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.583][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.626][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-06-05 21:01:02.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.648][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[2024-06-05 21:01:02.649][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-06-05 21:01:02.650][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:02.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-06-05 21:01:02.652][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:02.654][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml".
biodb.DEBUG[2024-06-05 21:01:02.655][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:02.656][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:02.658][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:02.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:02.676][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.677][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.679][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.685][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.687][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.688][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.689][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.693][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.694][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.696][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.697][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.701][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.702][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.703][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.704][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.709][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.710][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.712][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.717][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.718][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.720][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.721][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.722][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.724][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.725][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.729][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.730][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.732][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.737][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.738][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.740][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.741][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.745][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.746][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.748][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.749][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.753][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.754][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.756][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.757][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.799][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-06-05 21:01:02.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:02.821][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-06-05 21:01:02.822][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:02.824][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-06-05 21:01:02.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:02.827][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml".
biodb.DEBUG[2024-06-05 21:01:02.828][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:02.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:02.830][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:02.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.845][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:02.850][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.851][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.853][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.858][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.859][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.861][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.862][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:02.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:02.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.866][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.867][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.869][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:02.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:02.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.874][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.875][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.877][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:02.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:02.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.882][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.883][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.885][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:02.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.890][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.891][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:02.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.892][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.894][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.895][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.897][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.898][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:02.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.902][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.903][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.904][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:02.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.910][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.911][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.912][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.914][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:02.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:02.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.918][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.919][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.921][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.923][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:02.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:02.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.927][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.928][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.930][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:02.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:02.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:02.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:02.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:02.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.973][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-06-05 21:01:02.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:02.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:02.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:02.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:02.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:02.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:02.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:02.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:02.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:02.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:02.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:02.996][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-06-05 21:01:02.997][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:02.998][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-06-05 21:01:03.000][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:03.001][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml".
biodb.DEBUG[2024-06-05 21:01:03.002][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:03.003][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:03.005][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:03.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.023][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.024][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.031][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:03.032][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:03.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.034][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.036][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:03.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:03.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.040][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:03.041][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:03.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.042][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:03.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:03.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.048][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:03.049][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:03.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.051][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.052][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:03.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:03.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.056][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.057][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.058][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.064][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:03.065][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:03.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.066][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.068][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:03.069][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.069][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.070][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.072][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:03.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.075][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.076][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.078][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.083][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:03.084][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:03.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.086][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.087][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:03.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:03.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.091][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:03.092][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:03.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.094][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.095][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:03.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:03.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.099][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:03.100][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:03.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.102][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.103][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:03.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:03.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.145][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-06-05 21:01:03.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:03.167][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-06-05 21:01:03.168][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:03.170][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-06-05 21:01:03.171][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:03.172][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml".
biodb.DEBUG[2024-06-05 21:01:03.173][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:03.175][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:03.176][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:03.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.194][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.195][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.197][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.202][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:03.203][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:03.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.205][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.206][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:03.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:03.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.210][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:03.211][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:03.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.213][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:03.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:03.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:03.220][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:03.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.221][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:03.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:03.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.226][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.227][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.229][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.234][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:03.235][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:03.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.237][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.238][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:03.239][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.241][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.242][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:03.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.246][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.247][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.249][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.254][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:03.255][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:03.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.257][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:03.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:03.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.262][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:03.263][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:03.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.265][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.266][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:03.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:03.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.270][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:03.271][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:03.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.272][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.274][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:03.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:03.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:03.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.316][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-06-05 21:01:03.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.344][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:03.348][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:03.349][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-05 21:01:03.350][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:03.352][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-05 21:01:03.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.393][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.420][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.450][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.TRACE[2024-06-05 21:01:03.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.499][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.522][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.523][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.565][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.573][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.617][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[2024-06-05 21:01:03.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.630][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.683][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.747][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.765][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.769][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.776][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.777][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.TRACE[2024-06-05 21:01:03.778][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.818][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:03.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:03.893][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:03.897][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:03.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2024-06-05 21:01:03.899][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:03.901][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2024-06-05 21:01:03.904][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:03.907][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:03.908][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2024-06-05 21:01:03.909][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:03.911][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2024-06-05 21:01:03.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:03.923][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-06-05 21:01:03.924][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:03.926][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-06-05 21:01:03.927][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:03.929][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2024-06-05 21:01:03.930][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:03.931][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:03.932][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:03.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:03.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:03.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:03.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:03.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:03.941][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:03.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:03.944][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.945][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.947][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:03.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:03.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.952][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:03.953][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:03.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.955][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.956][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:03.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:03.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.960][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:03.961][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:03.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.963][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.964][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:03.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:03.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.968][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:03.969][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:03.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.971][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:03.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:03.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.976][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.977][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.978][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:03.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.983][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:03.984][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:03.985][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.986][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.987][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:03.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:03.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.991][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:03.992][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.994][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.995][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:03.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:03.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:03.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:03.999][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.000][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.002][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.007][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:04.008][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:04.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.010][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:04.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:04.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.015][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:04.016][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:04.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.018][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.019][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:04.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:04.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.023][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:04.024][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:04.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.026][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.027][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:04.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:04.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.077][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-06-05 21:01:04.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.099][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.TRACE[2024-06-05 21:01:04.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:04.122][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-06-05 21:01:04.123][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:04.125][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-06-05 21:01:04.127][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:04.129][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2024-06-05 21:01:04.131][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:04.133][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:04.134][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:04.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.153][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.155][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.157][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.164][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:04.166][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:04.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.168][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.170][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:04.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:04.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.176][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:04.178][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:04.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.180][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.182][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:04.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:04.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.188][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:04.190][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:04.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.193][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.195][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:04.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:04.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.202][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:04.203][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:04.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.206][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.208][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:04.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:04.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.214][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:04.216][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:04.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.218][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.220][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:04.222][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:04.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.225][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.226][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:04.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:04.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.233][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.234][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.237][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.243][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:04.244][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:04.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.246][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.247][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:04.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:04.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.251][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:04.252][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:04.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.254][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.255][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:04.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:04.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.264][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:04.266][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:04.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.267][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.269][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:04.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:04.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:04.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:04.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:04.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.311][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-06-05 21:01:04.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.338][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:04.342][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:04.343][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-05 21:01:04.344][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:04.345][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-05 21:01:04.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.357][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.TRACE[2024-06-05 21:01:04.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.378][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.TRACE[2024-06-05 21:01:04.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.441][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[2024-06-05 21:01:04.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.469][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.483][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.491][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.TRACE[2024-06-05 21:01:04.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.554][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.555][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[2024-06-05 21:01:04.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.602][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.625][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.645][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[2024-06-05 21:01:04.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.710][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[2024-06-05 21:01:04.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.719][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.753][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.TRACE[2024-06-05 21:01:04.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.797][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.836][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:04.840][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:04.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-06-05 21:01:04.843][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:04.844][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-06-05 21:01:04.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.862][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.870][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.871][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.877][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.940][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.TRACE[2024-06-05 21:01:04.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.965][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.977][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:04.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:04.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:04.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:04.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:04.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:04.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:04.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:04.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:04.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:04.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:04.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.020][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.106][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.108][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.146][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.208][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.219][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.274][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.282][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.314][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.TRACE[2024-06-05 21:01:05.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.339][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-05 21:01:05.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-05 21:01:05.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-05 21:01:05.350][biodb::testThat]
biodb.INFO [2024-06-05 21:01:05.351][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-06-05 21:01:05.352][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:05.353][biodb::testThat]
biodb.TRACE[2024-06-05 21:01:05.355][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-05 21:01:05.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-05 21:01:05.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:05.389][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:05.392][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:05.393][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-05 21:01:05.394][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:05.396][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-05 21:01:05.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.420][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:05.423][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:05.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-05 21:01:05.425][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:05.427][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-05 21:01:05.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.438][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[2024-06-05 21:01:05.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:05.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.472][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-05 21:01:05.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.490][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.498][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.498][private$selectFields]
biodb.TRACE[2024-06-05 21:01:05.499][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:05.500][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:05.501][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.502][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.503][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.505][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.506][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.507][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.509][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.510][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.511][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.511][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.513][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.514][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.515][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:05.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.537][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-05 21:01:05.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.555][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.556][private$selectFields]
biodb.TRACE[2024-06-05 21:01:05.557][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:05.558][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:05.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.560][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.561][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.563][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.565][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.567][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.567][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.568][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.569][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.572][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.573][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:05.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.586][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-05 21:01:05.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:05.597][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.604][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.605][private$selectFields]
biodb.TRACE[2024-06-05 21:01:05.606][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:05.607][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:05.608][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.609][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.610][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.611][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.612][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.613][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.615][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.616][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.617][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:05.618][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.619][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.621][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.622][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:05.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:05.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.634][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-05 21:01:05.635][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-05 21:01:05.636][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-05 21:01:05.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:05.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:05.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:05.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:05.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:05.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:05.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:05.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:05.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:05.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:05.728][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[2024-06-05 21:01:05.731][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.INFO [2024-06-05 21:01:05.734][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-06-05 21:01:05.735][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:05.736][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:05.738][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:06.140][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:06.542][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:06.545][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-05 21:01:06.549][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-05 21:01:06.552][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:06.556][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:06.557][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:06.559][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:06.969][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:07.414][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:07.417][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-05 21:01:07.421][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-05 21:01:07.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:07.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:07.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:07.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:07.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:07.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:07.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:07.434][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.442][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:07.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:07.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:07.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:07.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:07.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:07.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:07.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:07.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:07.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:07.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:07.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:07.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:07.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:07.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:07.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:07.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:07.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:07.524][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-05 21:01:07.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:07.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:07.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:07.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:07.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:07.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:07.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:07.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.567][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.568][private$selectFields]
biodb.TRACE[2024-06-05 21:01:07.568][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:07.569][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:07.570][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.572][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.574][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.575][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.576][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.578][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.579][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.580][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.581][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.582][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.583][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.584][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.585][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:07.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.598][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-05 21:01:07.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:07.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:07.601][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:07.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:07.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:07.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:07.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:07.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.656][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.657][private$selectFields]
biodb.TRACE[2024-06-05 21:01:07.658][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:07.659][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:07.660][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.661][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.662][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.664][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.665][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.666][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.668][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.669][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.679][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.680][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.681][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.683][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.683][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:07.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.696][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-05 21:01:07.697][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:07.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:07.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:07.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:07.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:07.705][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:07.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:07.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.714][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.715][private$selectFields]
biodb.TRACE[2024-06-05 21:01:07.716][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:07.717][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:07.718][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.719][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.720][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.721][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.722][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.723][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.725][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.726][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.727][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:07.728][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.729][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.731][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.732][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:07.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:07.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.744][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-05 21:01:07.745][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-05 21:01:07.746][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-05 21:01:07.754][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-05 21:01:07.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-05 21:01:07.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-05 21:01:07.760][biodb::testThat]
biodb.INFO [2024-06-05 21:01:07.761][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-06-05 21:01:07.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:07.763][biodb::testThat]
biodb.TRACE[2024-06-05 21:01:07.766][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-05 21:01:07.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-05 21:01:07.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:07.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:07.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:07.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:07.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:07.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:07.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:07.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:07.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:07.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:07.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:07.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:07.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:07.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:07.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:07.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:07.800][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:07.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:07.804][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:07.808][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:07.809][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:07.810][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:08.219][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:08.637][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-06-05 21:01:08.642][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-06-05 21:01:08.646][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-06-05 21:01:08.656][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-06-05 21:01:08.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:08.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:08.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:08.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:08.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:08.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:08.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:08.690][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:08.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:08.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:08.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:08.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:08.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:08.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:08.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:08.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:08.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:08.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:08.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:08.710][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:08.714][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:08.716][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:08.718][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:09.128][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:09.578][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:09.583][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-06-05 21:01:09.592][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-06-05 21:01:09.598][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:09.600][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:09.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:09.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:09.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:09.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:09.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:09.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:09.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:09.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:09.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:09.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:09.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:09.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:09.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:09.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:09.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:09.671][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-05 21:01:09.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:09.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:09.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:09.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:09.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:09.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:09.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:09.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.693][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.694][private$selectFields]
biodb.TRACE[2024-06-05 21:01:09.695][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:09.696][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:09.697][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.698][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.699][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.701][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.702][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.703][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.705][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.706][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.707][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.708][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.709][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.711][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.712][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:09.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.730][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.746][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-05 21:01:09.747][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:09.748][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:09.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:09.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:09.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:09.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:09.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:09.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.767][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.768][private$selectFields]
biodb.TRACE[2024-06-05 21:01:09.769][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:09.769][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:09.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.771][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.772][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.774][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.778][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.779][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.780][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.781][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.782][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.784][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.785][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:09.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.798][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-05 21:01:09.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:09.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:09.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:09.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:09.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:09.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:09.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:09.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.817][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.818][private$selectFields]
biodb.TRACE[2024-06-05 21:01:09.818][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:09.819][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:09.820][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.821][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.822][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.824][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.825][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.826][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.828][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.829][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.830][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:09.831][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.832][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.833][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.834][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:09.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:09.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.847][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-05 21:01:09.848][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-05 21:01:09.849][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-05 21:01:09.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:09.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:09.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:09.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:09.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:09.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:09.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:09.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:09.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:09.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:09.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:09.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:09.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:09.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:09.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:09.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:09.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:09.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:09.885][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:09.888][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:09.889][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:09.891][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:10.294][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:10.738][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:10.742][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-06-05 21:01:10.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-06-05 21:01:10.772][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:10.780][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:10.782][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:10.786][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:11.220][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:11.661][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:11.666][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-06-05 21:01:11.674][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-06-05 21:01:11.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:11.682][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:11.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:11.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:11.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:11.698][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:11.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:11.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.716][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:11.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:11.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:11.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:11.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:11.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:11.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:11.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:11.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:11.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:11.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:11.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:11.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:11.757][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:11.758][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[2024-06-05 21:01:11.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:11.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:11.771][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-05 21:01:11.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:11.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:11.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:11.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:11.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:11.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:11.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:11.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.790][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.790][private$selectFields]
biodb.TRACE[2024-06-05 21:01:11.791][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:11.792][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:11.793][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.795][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.797][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.798][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.799][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.801][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.802][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.803][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.803][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.804][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.806][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.807][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:11.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.820][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-05 21:01:11.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:11.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:11.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:11.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:11.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:11.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:11.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:11.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.838][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.839][private$selectFields]
biodb.TRACE[2024-06-05 21:01:11.840][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:11.841][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:11.842][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.843][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.844][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.846][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.847][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.848][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.850][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.851][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.861][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.862][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.864][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.866][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.867][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:11.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.880][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-05 21:01:11.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:11.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:11.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:11.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:11.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:11.889][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:11.890][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[2024-06-05 21:01:11.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.898][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.899][private$selectFields]
biodb.TRACE[2024-06-05 21:01:11.900][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:11.901][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:11.902][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.903][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.904][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.906][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.907][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.909][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.910][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.911][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:11.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.913][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.915][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.916][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:11.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:11.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.928][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-05 21:01:11.929][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-05 21:01:11.930][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-05 21:01:11.938][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-05 21:01:11.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-05 21:01:11.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-05 21:01:11.944][biodb::testThat]
biodb.INFO [2024-06-05 21:01:11.945][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-06-05 21:01:11.946][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:11.947][biodb::testThat]
biodb.TRACE[2024-06-05 21:01:11.950][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-06-05 21:01:11.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-06-05 21:01:11.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:11.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:11.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:11.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:11.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:11.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:11.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:11.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:11.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:11.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:11.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:11.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:11.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:11.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:11.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:11.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:11.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:11.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:11.984][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:11.987][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:11.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-06-05 21:01:11.989][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:11.990][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-06-05 21:01:11.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:11.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:11.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:11.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:12.015][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:12.018][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:12.019][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-06-05 21:01:12.020][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:12.021][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-06-05 21:01:12.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.037][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:12.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.060][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:12.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:12.071][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-05 21:01:12.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.089][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.090][private$selectFields]
biodb.TRACE[2024-06-05 21:01:12.091][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:12.092][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:12.093][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.095][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.097][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.098][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.099][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.101][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.102][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.106][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.107][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:12.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.120][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-06-05 21:01:12.121][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.128][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.138][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.139][private$selectFields]
biodb.TRACE[2024-06-05 21:01:12.139][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:12.140][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:12.141][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.142][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.143][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.145][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.146][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.149][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.150][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.151][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.151][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.152][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.154][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.155][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.168][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-05 21:01:12.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.187][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.188][private$selectFields]
biodb.TRACE[2024-06-05 21:01:12.194][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:12.195][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:12.196][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.198][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.199][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.201][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.202][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.203][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.205][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.207][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.207][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.209][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.210][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.211][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:12.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.225][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-06-05 21:01:12.225][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-05 21:01:12.226][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-05 21:01:12.243][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:12.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.269][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.271][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:12.274][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:12.277][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:12.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-06-05 21:01:12.280][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:12.281][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-06-05 21:01:12.284][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:12.287][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:12.288][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-06-05 21:01:12.289][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:12.290][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-06-05 21:01:12.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:12.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:12.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:12.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:12.359][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-06-05 21:01:12.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.376][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.377][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[2024-06-05 21:01:12.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.387][private$selectFields]
biodb.TRACE[2024-06-05 21:01:12.388][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:12.389][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:12.389][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.391][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.392][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.394][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.395][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.396][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.398][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.399][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.400][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.401][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.404][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.405][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:12.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.418][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-06-05 21:01:12.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.433][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.437][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.438][private$selectFields]
biodb.TRACE[2024-06-05 21:01:12.439][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:12.440][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:12.441][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.442][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.443][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.444][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.445][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.446][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.449][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.450][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.451][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.452][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.454][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.454][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:12.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.467][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-06-05 21:01:12.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:12.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.486][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.487][private$selectFields]
biodb.TRACE[2024-06-05 21:01:12.488][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-06-05 21:01:12.489][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-06-05 21:01:12.490][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.491][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.492][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.494][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.495][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.497][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.498][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.499][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.500][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-06-05 21:01:12.501][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.502][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.503][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.504][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.505][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-06-05 21:01:12.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:12.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:12.518][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-06-05 21:01:12.519][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-06-05 21:01:12.520][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-06-05 21:01:12.545][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-06-05 21:01:12.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-06-05 21:01:12.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:12.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-05 21:01:12.552][biodb::testThat]
biodb.INFO [2024-06-05 21:01:12.553][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-06-05 21:01:12.554][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:12.554][biodb::testThat]
biodb.DEBUG[2024-06-05 21:01:12.556][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-06-05 21:01:12.557][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:12.559][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-06-05 21:01:12.560][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:01:12.561][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:01:12.562][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:12.563][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:01:12.564][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:01:12.565][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:01:12.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:12.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:12.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:12.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:12.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:12.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:12.576][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[2024-06-05 21:01:12.577][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-06-05 21:01:12.580][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:12.581][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:12.582][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-06-05 21:01:12.983][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-06-05 21:01:13.387][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:13.392][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-06-05 21:01:13.399][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-06-05 21:01:13.405][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-06-05 21:01:13.408][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:01:13.411][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:13.414][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:13.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:13.420][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:13.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:13.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:13.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:13.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:13.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:13.440][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.441][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.444][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.452][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:13.454][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:13.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.456][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.458][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:13.459][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:13.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.462][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.463][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:13.464][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:13.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.467][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.468][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:13.469][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:13.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.473][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:13.474][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:13.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.475][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.477][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:13.478][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:13.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.480][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.481][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:13.482][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:13.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.484][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.485][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:13.486][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:13.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.488][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.489][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:13.490][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:13.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.492][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.493][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:13.494][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:13.495][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.496][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:13.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:13.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:13.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:13.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:13.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:13.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.523][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:13.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:13.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:13.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:13.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:13.534][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-06-05 21:01:13.535][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-06-05 21:01:13.547][biodb::testThat]
biodb.INFO [2024-06-05 21:01:13.551][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-06-05 21:01:13.552][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:13.553][biodb::testThat]
biodb.DEBUG[2024-06-05 21:01:13.562][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-06-05 21:01:13.563][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-06-05 21:01:13.564][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-06-05 21:01:13.565][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-06-05 21:01:13.567][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-06-05 21:01:13.568][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:01:13.569][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:13.570][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:01:13.571][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:01:13.572][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:01:13.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:13.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:13.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:13.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:13.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:13.583][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:13.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:13.585][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-06-05 21:01:13.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:13.588][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:13.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-06-05 21:01:13.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-06-05 21:01:14.417][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:14.421][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-06-05 21:01:14.428][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-06-05 21:01:14.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:14.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:14.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:14.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:14.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:14.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:14.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:14.453][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-06-05 21:01:14.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:14.461][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:14.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-06-05 21:01:14.890][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-06-05 21:01:15.335][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:15.341][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-06-05 21:01:15.348][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-06-05 21:01:15.351][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:15.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:15.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:15.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:15.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:15.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:15.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:15.373][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-06-05 21:01:15.379][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:15.381][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:15.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-06-05 21:01:15.809][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-06-05 21:01:16.246][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:16.251][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-06-05 21:01:16.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-06-05 21:01:16.263][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-06-05 21:01:16.267][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:01:16.270][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-06-05 21:01:16.272][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:16.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:16.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:16.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:16.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:16.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:16.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:16.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:16.298][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.299][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.302][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.310][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:16.312][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:16.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.314][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.316][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:16.317][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:16.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.320][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.321][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:16.323][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:16.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.325][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.326][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.327][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.329][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.331][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.332][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.334][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.335][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:16.336][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:16.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.338][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.339][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.340][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.342][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.343][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:16.344][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:16.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.346][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.347][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:16.348][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:16.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.350][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.351][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:16.352][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:16.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.354][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:16.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:16.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:16.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:16.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:16.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:16.403][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:16.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:16.406][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.407][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.409][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.414][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:16.415][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:16.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.417][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.418][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:16.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:16.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.422][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:16.423][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:16.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.424][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:16.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:16.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.429][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:16.430][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:16.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.432][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:16.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:16.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.437][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.438][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.440][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.445][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.446][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.448][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.449][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.453][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:16.453][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:16.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.455][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.456][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:16.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:16.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.460][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.461][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.463][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.468][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:16.469][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:16.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.471][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.472][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:16.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:16.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.476][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:16.477][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:16.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.478][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.480][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:16.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:16.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.483][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:16.484][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:16.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.486][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.487][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:16.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:16.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:16.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:16.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:16.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:16.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:16.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:16.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:16.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:16.535][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.536][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.538][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.543][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:16.544][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:16.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.546][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.547][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:16.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:16.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.551][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:16.552][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:16.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.554][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.555][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:16.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:16.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.559][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:16.560][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:16.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.561][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:16.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:16.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.567][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.568][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.569][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:16.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.574][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.575][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.577][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.578][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:16.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.582][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:16.583][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:16.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.585][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.586][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:16.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:16.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.590][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.591][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.593][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:16.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.598][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:16.599][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:16.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.601][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:16.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:16.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.606][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:16.607][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:16.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.609][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.610][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:16.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:16.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.614][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:16.615][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:16.616][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.617][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.618][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:16.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:16.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:16.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:16.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:16.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:16.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:16.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:16.683][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-06-05 21:01:16.683][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-06-05 21:01:16.684][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-06-05 21:01:16.702][biodb::testThat]
biodb.INFO [2024-06-05 21:01:16.703][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-06-05 21:01:16.704][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:16.705][biodb::testThat]
biodb.INFO [2024-06-05 21:01:16.727][biodb::testThat]
biodb.INFO [2024-06-05 21:01:16.728][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-06-05 21:01:16.729][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:16.730][biodb::testThat]
biodb.INFO [2024-06-05 21:01:16.738][biodb::testThat]
biodb.INFO [2024-06-05 21:01:16.739][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-06-05 21:01:16.740][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:16.741][biodb::testThat]
biodb.DEBUG[2024-06-05 21:01:16.743][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:16.747][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:16.748][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:16.750][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:17.213][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:17.780][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:17.782][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-06-05 21:01:17.785][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-06-05 21:01:17.795][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:17.796][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:17.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:17.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:17.799][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:17.800][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:17.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:17.802][ef$get] fields variable is a list.
biodb.INFO [2024-06-05 21:01:17.803][biodb::testThat]
biodb.INFO [2024-06-05 21:01:17.804][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-06-05 21:01:17.805][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:17.806][biodb::testThat]
biodb.ERROR[2024-06-05 21:01:17.818][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-06-05 21:01:17.833][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-06-05 21:01:17.846][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-05 21:01:17.847][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-05 21:01:17.848][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-05 21:01:17.849][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-05 21:01:17.849][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:17.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:17.851][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:17.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:17.853][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-05 21:01:17.863][biodb::testContext]
biodb.INFO [2024-06-05 21:01:17.864][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-05 21:01:17.865][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-06-05 21:01:17.866][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-05 21:01:17.867][biodb::testContext]
biodb.INFO [2024-06-05 21:01:17.869][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-05 21:01:17.870][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-05 21:01:17.874][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:17.875][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-05 21:01:17.876][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-05 21:01:17.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.879][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-05 21:01:17.889][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-05 21:01:17.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.893][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-05 21:01:17.894][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-05 21:01:17.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.898][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-05 21:01:17.899][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-05 21:01:17.900][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-05 21:01:17.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.903][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-05 21:01:17.904][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-05 21:01:17.905][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-05 21:01:17.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.907][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[2024-06-05 21:01:17.908][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-05 21:01:17.909][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-05 21:01:17.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.913][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-05 21:01:17.914][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-05 21:01:17.915][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-05 21:01:17.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.918][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-05 21:01:17.919][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-05 21:01:17.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.922][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-05 21:01:17.923][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-05 21:01:17.924][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-05 21:01:17.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.928][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-05 21:01:17.928][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-05 21:01:17.929][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-05 21:01:17.930][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-05 21:01:17.931][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-05 21:01:17.932][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-05 21:01:17.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.936][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-05 21:01:17.937][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-05 21:01:17.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.940][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-05 21:01:17.941][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-05 21:01:17.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.944][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-05 21:01:17.945][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-05 21:01:17.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.949][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-05 21:01:17.950][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-05 21:01:17.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.953][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-05 21:01:17.954][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-05 21:01:17.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.956][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[2024-06-05 21:01:17.957][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-05 21:01:17.958][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-05 21:01:17.961][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-05 21:01:17.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:17.965][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-05 21:01:17.966][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-05 21:01:17.967][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-05 21:01:17.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:17.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:17.969][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[2024-06-05 21:01:17.970][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-05 21:01:17.972][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:17.973][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-05 21:01:17.974][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:17.975][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:17.976][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:17.977][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:17.978][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:17.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:17.980][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-05 21:01:17.981][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:17.982][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:17.982][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-05 21:01:17.983][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:17.984][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:17.985][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:17.986][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:17.986][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:17.986][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:17.986][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-05 21:01:17.986][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-05 21:01:17.987][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:17.988][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:17.989][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:17.990][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:17.991][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:17.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:17.992][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:17.993][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:17.994][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:17.995][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:17.996][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:17.997][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:17.998][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-05 21:01:18.000][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.001][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-05 21:01:18.002][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.002][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:18.003][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.004][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.005][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.006][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.007][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-05 21:01:18.008][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:18.009][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.010][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-05 21:01:18.011][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:18.012][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.013][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.014][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:18.014][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:18.014][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:18.014][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-05 21:01:18.014][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-05 21:01:18.015][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:18.016][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:18.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:18.017][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:18.018][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:18.019][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:18.020][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.021][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:18.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:18.023][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.024][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.025][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-05 21:01:18.027][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.028][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-05 21:01:18.029][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:18.031][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.032][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.033][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.034][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.035][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-05 21:01:18.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:18.036][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.037][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-05 21:01:18.038][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:18.039][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.040][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.041][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.048][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:18.049][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:18.050][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:18.051][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:18.052][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:18.053][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:18.053][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.054][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.055][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:18.056][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:18.057][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.058][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.059][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-05 21:01:18.061][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.062][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-05 21:01:18.063][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.064][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:18.065][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.066][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.067][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.067][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.068][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-05 21:01:18.069][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:18.070][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.071][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-05 21:01:18.072][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:18.073][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.074][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.075][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.076][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:18.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:18.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:18.079][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:18.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:18.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:18.081][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.082][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:18.084][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:18.085][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.086][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:18.087][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:18.088][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.130][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.DEBUG[2024-06-05 21:01:18.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.146][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[2024-06-05 21:01:18.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.151][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[2024-06-05 21:01:18.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.160][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-05 21:01:18.162][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-05 21:01:18.163][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-05 21:01:18.164][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-05 21:01:18.166][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-05 21:01:18.167][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-05 21:01:18.168][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-05 21:01:18.170][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-05 21:01:18.171][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-05 21:01:18.172][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-05 21:01:18.174][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-05 21:01:18.175][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-05 21:01:18.176][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-05 21:01:18.178][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-05 21:01:18.179][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-05 21:01:18.180][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-05 21:01:18.181][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-05 21:01:18.183][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-05 21:01:18.184][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-05 21:01:18.185][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-05 21:01:18.187][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-05 21:01:18.188][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-05 21:01:18.189][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-05 21:01:18.191][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-05 21:01:18.192][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-05 21:01:18.193][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-05 21:01:18.194][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-05 21:01:18.196][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-05 21:01:18.202][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-05 21:01:18.204][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-05 21:01:18.205][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-05 21:01:18.206][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-05 21:01:18.208][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-05 21:01:18.209][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-05 21:01:18.210][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-05 21:01:18.212][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-05 21:01:18.213][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-05 21:01:18.214][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-05 21:01:18.215][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-05 21:01:18.217][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-05 21:01:18.218][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-05 21:01:18.219][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-05 21:01:18.221][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-05 21:01:18.222][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-05 21:01:18.223][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-05 21:01:18.225][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-05 21:01:18.226][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-05 21:01:18.227][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-05 21:01:18.228][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-05 21:01:18.230][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-05 21:01:18.231][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-05 21:01:18.232][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-05 21:01:18.234][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-05 21:01:18.235][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-05 21:01:18.236][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-05 21:01:18.237][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-05 21:01:18.239][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-05 21:01:18.240][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-05 21:01:18.241][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-05 21:01:18.243][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-05 21:01:18.244][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-05 21:01:18.245][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-05 21:01:18.247][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-05 21:01:18.248][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-05 21:01:18.249][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-05 21:01:18.250][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-05 21:01:18.252][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-05 21:01:18.253][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-05 21:01:18.254][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-05 21:01:18.256][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-05 21:01:18.257][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-05 21:01:18.258][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-05 21:01:18.259][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-05 21:01:18.261][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-05 21:01:18.262][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-05 21:01:18.263][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-05 21:01:18.264][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-05 21:01:18.266][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-05 21:01:18.267][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-05 21:01:18.268][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-05 21:01:18.270][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-05 21:01:18.271][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-05 21:01:18.272][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-05 21:01:18.274][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-05 21:01:18.275][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-05 21:01:18.276][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:18.277][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.279][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.332][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[2024-06-05 21:01:18.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.338][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[2024-06-05 21:01:18.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.344][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[2024-06-05 21:01:18.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:18.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:18.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:18.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:18.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:18.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:18.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:18.387][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-05 21:01:18.388][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-05 21:01:18.390][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.391][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.392][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.393][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:18.394][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.395][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.396][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.397][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-05 21:01:18.398][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-05 21:01:18.399][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:18.400][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.401][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-05 21:01:18.401][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-05 21:01:18.402][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-05 21:01:18.404][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:18.404][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:18.404][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:18.404][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:18.405][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-05 21:01:18.406][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:18.407][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:18.408][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:18.409][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:18.410][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:18.411][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:18.412][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:01:18.412][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-05 21:01:18.413][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:18.413][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:18.414][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:18.415][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-05 21:01:18.415][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-05 21:01:18.417][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-05 21:01:18.418][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-05 21:01:18.420][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-05 21:01:18.421][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-05 21:01:18.422][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-05 21:01:18.424][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-05 21:01:18.427][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-05 21:01:18.428][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-05 21:01:18.429][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-05 21:01:18.430][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-05 21:01:18.431][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-05 21:01:18.432][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-05 21:01:18.434][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-05 21:01:18.435][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-05 21:01:18.436][biodb::testThat]
biodb.INFO [2024-06-05 21:01:18.437][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-06-05 21:01:18.438][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:18.438][biodb::testThat]
biodb.DEBUG[2024-06-05 21:01:18.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-05 21:01:18.445][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:18.446][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:18.447][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-06-05 21:01:18.845][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-06-05 21:01:19.418][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:19.422][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-06-05 21:01:19.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-06-05 21:01:19.438][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:19.445][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:19.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:19.451][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:19.891][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:20.297][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:20.302][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-06-05 21:01:20.310][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-06-05 21:01:20.315][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:20.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:20.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:20.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:20.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:20.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:20.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:20.339][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:20.345][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:20.347][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:20.349][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:20.776][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:21.215][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:21.217][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-06-05 21:01:21.220][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-06-05 21:01:21.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:21.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:21.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:21.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:21.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:21.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:21.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:21.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:21.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:21.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:21.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:21.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:21.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:21.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:21.464][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:21.467][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:21.468][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-05 21:01:21.469][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:21.470][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-05 21:01:21.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:21.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:21.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:21.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:21.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:21.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:21.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:21.482][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:21.485][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:21.486][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-05 21:01:21.487][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:21.489][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-05 21:01:21.490][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:21.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:21.492][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:21.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:21.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:21.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:21.499][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[2024-06-05 21:01:21.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:21.500][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:21.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:21.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:21.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:21.507][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:21.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:21.512][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:21.515][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:21.516][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-06-05 21:01:21.517][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:21.518][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-06-05 21:01:21.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:21.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:21.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:21.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:21.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:21.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:21.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:21.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:21.533][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:21.534][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-06-05 21:01:21.535][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:21.536][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-06-05 21:01:21.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:21.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:21.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:21.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:21.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:21.545][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:21.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:21.548][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:21.551][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:21.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:21.553][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:21.957][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:22.355][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:22.357][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-06-05 21:01:22.361][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-06-05 21:01:22.363][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:22.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:22.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:22.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:22.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:22.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:22.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-05 21:01:22.377][biodb::testThat]
biodb.INFO [2024-06-05 21:01:22.378][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-06-05 21:01:22.379][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:22.380][biodb::testThat]
biodb.DEBUG[2024-06-05 21:01:22.383][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:22.387][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:22.388][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:22.390][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:22.793][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:23.199][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:23.201][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-06-05 21:01:23.205][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-06-05 21:01:23.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:23.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:23.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:23.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:23.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:23.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:23.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:23.222][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:23.226][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:23.227][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:23.229][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:23.644][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:24.063][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:24.069][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-06-05 21:01:24.079][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-06-05 21:01:24.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:24.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-05 21:01:24.116][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-05 21:01:24.118][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-05 21:01:24.120][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-05 21:01:24.122][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-05 21:01:24.124][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.127][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.130][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-05 21:01:24.136][biodb::testContext]
biodb.INFO [2024-06-05 21:01:24.137][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-05 21:01:24.139][biodb::testContext] Test context - Test web services
biodb.INFO [2024-06-05 21:01:24.140][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-05 21:01:24.141][biodb::testContext]
biodb.INFO [2024-06-05 21:01:24.144][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-05 21:01:24.146][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-05 21:01:24.151][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:24.152][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-05 21:01:24.153][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-05 21:01:24.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.157][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-05 21:01:24.158][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-05 21:01:24.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.162][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-05 21:01:24.163][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-05 21:01:24.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.167][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-05 21:01:24.168][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-05 21:01:24.169][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-05 21:01:24.170][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.173][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-05 21:01:24.174][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-05 21:01:24.175][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-05 21:01:24.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.179][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-05 21:01:24.180][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-05 21:01:24.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.184][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-05 21:01:24.185][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-05 21:01:24.186][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-05 21:01:24.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.190][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-05 21:01:24.191][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-05 21:01:24.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.194][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-05 21:01:24.195][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-05 21:01:24.196][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-05 21:01:24.197][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.200][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-05 21:01:24.201][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-05 21:01:24.202][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-05 21:01:24.203][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-05 21:01:24.204][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-05 21:01:24.205][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-05 21:01:24.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.209][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-05 21:01:24.210][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-05 21:01:24.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.214][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-05 21:01:24.215][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-05 21:01:24.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.219][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-05 21:01:24.220][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-05 21:01:24.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.224][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-05 21:01:24.225][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-05 21:01:24.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.241][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-05 21:01:24.242][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-05 21:01:24.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.245][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-05 21:01:24.246][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-05 21:01:24.249][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-05 21:01:24.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.252][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-05 21:01:24.253][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-05 21:01:24.254][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-05 21:01:24.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.258][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-05 21:01:24.259][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.260][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-05 21:01:24.261][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.262][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:24.263][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.264][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.265][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.266][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.267][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-05 21:01:24.267][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:24.268][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.269][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-05 21:01:24.270][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:24.271][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.272][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.273][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:24.273][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:24.273][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:24.273][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-05 21:01:24.273][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-05 21:01:24.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:24.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.276][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:24.277][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.279][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.280][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.281][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:24.282][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:24.282][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.283][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.284][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-05 21:01:24.286][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.287][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-05 21:01:24.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.289][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:24.290][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.290][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.291][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.292][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.293][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-05 21:01:24.294][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:24.295][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.296][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-05 21:01:24.297][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:24.298][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.298][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.299][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:24.299][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:24.299][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:24.299][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-05 21:01:24.299][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-05 21:01:24.300][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:24.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.303][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:24.304][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.306][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.306][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.307][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:24.308][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:24.309][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.310][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.311][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-05 21:01:24.313][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.314][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-05 21:01:24.315][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.315][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:24.316][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.317][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.318][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.319][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.320][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-05 21:01:24.321][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:24.322][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.323][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-05 21:01:24.323][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:24.324][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.325][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.326][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.327][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:24.328][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.329][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.330][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:24.330][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.331][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.332][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.333][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.334][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:24.335][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:24.335][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.336][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.337][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-05 21:01:24.339][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.340][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-05 21:01:24.341][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.342][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:24.343][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.343][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.344][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.346][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-05 21:01:24.347][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:24.348][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.349][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-05 21:01:24.350][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:24.351][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.351][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.352][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.353][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:24.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.355][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:24.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.358][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.358][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.359][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.360][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:24.361][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:24.362][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.363][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:24.364][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:24.365][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.374][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[2024-06-05 21:01:24.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.391][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.DEBUG[2024-06-05 21:01:24.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.432][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[2024-06-05 21:01:24.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.437][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-05 21:01:24.438][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-05 21:01:24.440][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-05 21:01:24.441][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-05 21:01:24.442][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-05 21:01:24.444][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-05 21:01:24.445][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-05 21:01:24.446][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-05 21:01:24.448][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-05 21:01:24.449][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-05 21:01:24.450][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-05 21:01:24.451][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-05 21:01:24.453][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-05 21:01:24.454][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-05 21:01:24.455][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-05 21:01:24.457][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-05 21:01:24.458][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-05 21:01:24.459][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-05 21:01:24.460][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-05 21:01:24.462][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-05 21:01:24.463][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-05 21:01:24.464][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-05 21:01:24.466][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-05 21:01:24.467][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-05 21:01:24.468][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-05 21:01:24.469][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-05 21:01:24.471][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-05 21:01:24.472][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-05 21:01:24.473][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-05 21:01:24.475][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-05 21:01:24.476][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-05 21:01:24.477][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-05 21:01:24.479][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-05 21:01:24.480][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-05 21:01:24.481][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-05 21:01:24.482][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-05 21:01:24.484][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-05 21:01:24.485][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-05 21:01:24.486][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-05 21:01:24.488][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-05 21:01:24.489][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-05 21:01:24.490][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-05 21:01:24.491][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-05 21:01:24.493][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-05 21:01:24.494][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-05 21:01:24.495][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-05 21:01:24.497][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-05 21:01:24.498][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-05 21:01:24.499][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-05 21:01:24.501][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-05 21:01:24.502][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-05 21:01:24.503][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-05 21:01:24.505][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-05 21:01:24.506][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-05 21:01:24.507][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-05 21:01:24.509][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-05 21:01:24.510][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-05 21:01:24.511][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-05 21:01:24.513][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-05 21:01:24.514][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-05 21:01:24.515][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-05 21:01:24.517][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-05 21:01:24.518][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-05 21:01:24.519][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-05 21:01:24.526][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-05 21:01:24.527][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-05 21:01:24.529][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-05 21:01:24.530][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-05 21:01:24.531][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-05 21:01:24.532][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-05 21:01:24.534][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-05 21:01:24.535][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-05 21:01:24.536][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-05 21:01:24.537][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-05 21:01:24.539][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-05 21:01:24.540][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-05 21:01:24.541][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-05 21:01:24.542][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-05 21:01:24.544][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-05 21:01:24.545][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-05 21:01:24.546][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-05 21:01:24.547][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-05 21:01:24.549][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-05 21:01:24.550][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-05 21:01:24.551][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-05 21:01:24.552][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:24.553][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.555][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.556][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.DEBUG[2024-06-05 21:01:24.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.601][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.607][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.617][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.DEBUG[2024-06-05 21:01:24.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.634][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[2024-06-05 21:01:24.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:24.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:24.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:24.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:24.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:24.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:24.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:24.653][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-05 21:01:24.654][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-05 21:01:24.656][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.657][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.658][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.659][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:24.660][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.661][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.662][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.663][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-05 21:01:24.663][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-05 21:01:24.664][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:24.665][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.666][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-05 21:01:24.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-05 21:01:24.668][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-05 21:01:24.669][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:24.670][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:24.670][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:24.670][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:24.671][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-05 21:01:24.672][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.674][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:24.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:24.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:24.676][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:24.677][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:01:24.677][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-05 21:01:24.678][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:24.679][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:24.680][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:24.681][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-05 21:01:24.681][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-05 21:01:24.682][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-05 21:01:24.683][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-05 21:01:24.685][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-05 21:01:24.686][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-05 21:01:24.688][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-05 21:01:24.689][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-05 21:01:24.692][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-05 21:01:24.693][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-05 21:01:24.694][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-05 21:01:24.695][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-05 21:01:24.696][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-05 21:01:24.697][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-05 21:01:24.699][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-05 21:01:24.699][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-05 21:01:24.701][biodb::testThat]
biodb.INFO [2024-06-05 21:01:24.702][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-06-05 21:01:24.702][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:24.703][biodb::testThat]
biodb.DEBUG[2024-06-05 21:01:24.706][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-05 21:01:24.709][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:24.710][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-05 21:01:24.712][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:24.713][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-05 21:01:24.716][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:24.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:24.720][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:24.722][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-06-05 21:01:25.121][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-06-05 21:01:25.544][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:25.549][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-06-05 21:01:25.558][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-06-05 21:01:25.575][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-05 21:01:25.578][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-05 21:01:25.581][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-05 21:01:25.583][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-05 21:01:25.585][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:25.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:25.588][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.592][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.593][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.INFO [2024-06-05 21:01:25.599][biodb::testContext]
biodb.INFO [2024-06-05 21:01:25.601][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-05 21:01:25.602][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-06-05 21:01:25.604][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-05 21:01:25.605][biodb::testContext]
biodb.INFO [2024-06-05 21:01:25.608][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-06-05 21:01:25.611][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-06-05 21:01:25.616][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:25.617][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-05 21:01:25.618][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-05 21:01:25.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.622][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-05 21:01:25.624][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-05 21:01:25.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.628][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-05 21:01:25.629][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-05 21:01:25.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.633][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-05 21:01:25.634][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-05 21:01:25.635][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-05 21:01:25.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.639][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-05 21:01:25.640][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-05 21:01:25.641][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-05 21:01:25.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.644][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-05 21:01:25.645][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-05 21:01:25.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.648][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[2024-06-05 21:01:25.649][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-05 21:01:25.650][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-05 21:01:25.651][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-05 21:01:25.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.654][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-05 21:01:25.655][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-05 21:01:25.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.658][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[2024-06-05 21:01:25.659][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-05 21:01:25.660][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-05 21:01:25.661][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-05 21:01:25.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.664][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-05 21:01:25.665][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-05 21:01:25.666][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-05 21:01:25.667][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-05 21:01:25.668][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-05 21:01:25.669][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-05 21:01:25.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.673][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-05 21:01:25.683][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-05 21:01:25.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.687][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-05 21:01:25.688][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-05 21:01:25.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.690][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[2024-06-05 21:01:25.691][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-05 21:01:25.692][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-05 21:01:25.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.696][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-05 21:01:25.697][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-05 21:01:25.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.700][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-05 21:01:25.701][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-05 21:01:25.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.704][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-05 21:01:25.706][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-05 21:01:25.711][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-05 21:01:25.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.714][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-05 21:01:25.715][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-05 21:01:25.716][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-05 21:01:25.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.720][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-05 21:01:25.722][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.723][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-05 21:01:25.724][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.725][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:25.725][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.726][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.727][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.729][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-05 21:01:25.730][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:25.731][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.732][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-05 21:01:25.733][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:25.734][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.735][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.736][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:25.736][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:25.736][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:25.736][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-05 21:01:25.736][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-05 21:01:25.737][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:25.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:25.738][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:25.739][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:25.740][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:25.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:25.742][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.743][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.744][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:25.745][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:25.746][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.747][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.748][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-05 21:01:25.749][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.750][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-05 21:01:25.751][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.752][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:25.753][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.754][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.755][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.756][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.757][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-05 21:01:25.758][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:25.759][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.760][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-05 21:01:25.761][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:25.762][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.763][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.764][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:25.764][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:25.764][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:25.764][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-05 21:01:25.764][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-05 21:01:25.765][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:25.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:25.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:25.768][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:25.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:25.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:25.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.771][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.772][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:25.773][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:25.774][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.775][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.776][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-05 21:01:25.778][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.779][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-05 21:01:25.780][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.781][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:25.782][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.783][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.784][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.786][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.787][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-05 21:01:25.788][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:25.790][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.791][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-05 21:01:25.791][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:25.792][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.793][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.794][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.795][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:25.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:25.797][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:25.798][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:25.799][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:25.800][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:25.801][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.802][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.803][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:25.804][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:25.805][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.806][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.807][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-05 21:01:25.809][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.810][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-05 21:01:25.811][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.812][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:25.813][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.814][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.815][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.816][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.817][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-05 21:01:25.818][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:25.819][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.820][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-05 21:01:25.821][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:25.822][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.824][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:25.825][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.826][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-05 21:01:25.827][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:25.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:25.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:25.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:25.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:25.832][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:25.833][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.834][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:25.835][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:25.836][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:25.837][self$setPropertyValue]
biodb.DEBUG[2024-06-05 21:01:25.838][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:25.839][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.840][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[2024-06-05 21:01:25.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.880][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.DEBUG[2024-06-05 21:01:25.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.902][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[2024-06-05 21:01:25.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:25.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:25.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:25.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:25.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:25.918][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-05 21:01:25.919][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-05 21:01:25.921][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-05 21:01:25.922][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-05 21:01:25.924][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-05 21:01:25.925][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-05 21:01:25.926][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-05 21:01:25.928][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-05 21:01:25.929][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-05 21:01:25.931][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-05 21:01:25.932][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-05 21:01:25.934][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-05 21:01:25.935][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-05 21:01:25.937][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-05 21:01:25.938][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-05 21:01:25.939][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-05 21:01:25.941][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-05 21:01:25.942][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-05 21:01:25.944][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-05 21:01:25.945][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-05 21:01:25.947][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-05 21:01:25.948][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-05 21:01:25.950][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-05 21:01:25.951][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-05 21:01:25.953][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-05 21:01:25.954][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-05 21:01:25.956][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-05 21:01:25.957][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-05 21:01:25.959][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-05 21:01:25.960][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-05 21:01:25.962][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-05 21:01:25.963][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-05 21:01:25.964][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-05 21:01:25.966][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-05 21:01:25.967][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-05 21:01:25.969][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-05 21:01:25.970][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-05 21:01:25.971][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-05 21:01:25.973][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-05 21:01:25.974][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-05 21:01:25.976][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-05 21:01:25.977][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-05 21:01:25.978][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-05 21:01:25.980][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-05 21:01:25.981][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-05 21:01:25.983][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-05 21:01:25.984][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-05 21:01:25.985][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-05 21:01:25.987][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-05 21:01:25.988][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-05 21:01:25.995][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-05 21:01:25.997][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-05 21:01:25.998][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-05 21:01:25.999][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-05 21:01:26.001][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-05 21:01:26.002][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-05 21:01:26.003][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-05 21:01:26.004][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-05 21:01:26.006][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-05 21:01:26.007][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-05 21:01:26.009][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-05 21:01:26.011][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-05 21:01:26.013][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-05 21:01:26.014][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-05 21:01:26.016][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-05 21:01:26.017][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-05 21:01:26.018][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-05 21:01:26.020][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-05 21:01:26.021][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-05 21:01:26.023][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-05 21:01:26.024][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-05 21:01:26.026][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-05 21:01:26.027][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-05 21:01:26.028][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-05 21:01:26.030][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-05 21:01:26.031][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-05 21:01:26.033][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-05 21:01:26.034][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-05 21:01:26.036][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-05 21:01:26.037][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-05 21:01:26.038][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-05 21:01:26.040][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-05 21:01:26.041][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-05 21:01:26.042][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-05 21:01:26.044][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-06-05 21:01:26.045][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-05 21:01:26.046][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.048][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.048][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[2024-06-05 21:01:26.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.061][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.107][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[2024-06-05 21:01:26.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.118][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.128][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.DEBUG[2024-06-05 21:01:26.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-05 21:01:26.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.155][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-06-05 21:01:26.156][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-06-05 21:01:26.158][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:26.159][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-06-05 21:01:26.160][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:26.161][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-05 21:01:26.162][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:26.163][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-05 21:01:26.164][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:26.164][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-06-05 21:01:26.165][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-06-05 21:01:26.166][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-05 21:01:26.167][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:26.168][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-06-05 21:01:26.169][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-06-05 21:01:26.170][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-06-05 21:01:26.171][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-05 21:01:26.172][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-05 21:01:26.172][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-05 21:01:26.172][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-05 21:01:26.173][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-05 21:01:26.174][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:26.175][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:26.176][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-05 21:01:26.177][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-05 21:01:26.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-05 21:01:26.179][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-05 21:01:26.180][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:01:26.180][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-06-05 21:01:26.181][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-05 21:01:26.181][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-05 21:01:26.182][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-05 21:01:26.183][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-06-05 21:01:26.183][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-06-05 21:01:26.185][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-05 21:01:26.186][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-05 21:01:26.188][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-06-05 21:01:26.189][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-05 21:01:26.190][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-05 21:01:26.192][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-05 21:01:26.195][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-06-05 21:01:26.196][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-06-05 21:01:26.197][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-06-05 21:01:26.199][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-06-05 21:01:26.200][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-05 21:01:26.201][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-05 21:01:26.202][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-06-05 21:01:26.203][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-06-05 21:01:26.205][biodb::testThat]
biodb.INFO [2024-06-05 21:01:26.205][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-06-05 21:01:26.206][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-05 21:01:26.207][biodb::testThat]
biodb.DEBUG[2024-06-05 21:01:26.210][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-06-05 21:01:26.214][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:26.215][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-06-05 21:01:26.216][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:26.217][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-06-05 21:01:26.221][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-06-05 21:01:26.223][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-06-05 21:01:26.225][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-06-05 21:01:26.226][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-06-05 21:01:26.227][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-06-05 21:01:26.231][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-06-05 21:01:26.232][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-06-05 21:01:26.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-06-05 21:01:26.235][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-06-05 21:01:26.236][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-06-05 21:01:26.237][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-06-05 21:01:26.238][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-06-05 21:01:26.239][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-06-05 21:01:26.240][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-06-05 21:01:26.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:26.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:26.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:26.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:26.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:26.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:26.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-05 21:01:26.253][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-06-05 21:01:26.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-06-05 21:01:26.256][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-06-05 21:01:26.257][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-06-05 21:01:26.676][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-06-05 21:01:27.743][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-06-05 21:01:27.748][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-06-05 21:01:27.755][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-06-05 21:01:27.762][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-06-05 21:01:27.765][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-06-05 21:01:27.768][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-06-05 21:01:27.770][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-06-05 21:01:27.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-05 21:01:27.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:27.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:27.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:27.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:27.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:27.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-05 21:01:27.794][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.795][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.798][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.804][ef$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:27.806][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:27.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.808][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.809][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-06-05 21:01:27.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-06-05 21:01:27.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.823][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:27.824][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:27.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.826][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.827][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-05 21:01:27.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-05 21:01:27.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.831][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-05 21:01:27.832][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-05 21:01:27.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.834][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.835][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-05 21:01:27.836][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-05 21:01:27.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.838][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.839][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:27.840][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:27.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.842][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.844][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:27.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-06-05 21:01:27.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.848][ef$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:27.849][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:27.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.850][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.852][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-06-05 21:01:27.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-05 21:01:27.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.855][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:27.856][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:27.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.858][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.859][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:27.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-06-05 21:01:27.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.863][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:27.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:27.865][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.866][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-05 21:01:27.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-05 21:01:27.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.871][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:27.872][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:27.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.874][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.875][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-06-05 21:01:27.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-06-05 21:01:27.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.879][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:27.880][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:27.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.881][ef$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.883][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-06-05 21:01:27.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-06-05 21:01:27.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:27.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:27.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:27.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:27.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-06-05 21:01:27.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-06-05 21:01:27.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-05 21:01:27.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-05 21:01:27.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-05 21:01:27.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-05 21:01:27.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-05 21:01:27.922][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-06-05 21:01:27.926][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-05 21:01:27.927][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-06-05 21:01:27.928][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-06-05 21:01:27.929][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-05 21:01:27.930][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-05 21:01:27.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-05 21:01:27.931][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-05 21:01:27.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-05 21:01:27.933][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-05 21:01:27.934][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 375 ]
> 
> proc.time()
   user  system elapsed 
 21.743   0.868  47.759

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn1.0410.1632.184
ChebiEntry0.1510.0000.150