Multiple platform build/check report for BioC 3.19 - CHECK results for biodbChebi on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

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: 2024-10-16 22:08:15 -0400 (Wed, 16 Oct 2024)

EndedAt: 2024-10-16 22:10:27 -0400 (Wed, 16 Oct 2024)

EllapsedTime: 131.3 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 4.4.1 (2024-06-14)
* 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 22.04.5 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 [2024-10-16 22:08:58.278][biodb::testContext]
biodb.INFO [2024-10-16 22:08:58.280][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:08:58.282][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-16 22:08:58.283][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:08:58.284][biodb::testContext]
biodb.INFO [2024-10-16 22:08:58.291][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:08:58.293][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:08:58.301][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:08:58.303][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:08:58.304][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:08:58.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.308][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:08:58.328][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:08:58.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.332][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[2024-10-16 22:08:58.333][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:08:58.334][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:08:58.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.338][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:08:58.339][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:08:58.340][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:08:58.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.344][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:08:58.345][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:08:58.346][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:08:58.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.350][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:08:58.351][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:08:58.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.355][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:08:58.356][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:08:58.357][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:08:58.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.361][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:08:58.362][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:08:58.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.366][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:08:58.367][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:08:58.368][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:08:58.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.372][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:08:58.373][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:08:58.374][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:08:58.375][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:08:58.376][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:08:58.377][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:08:58.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.381][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:08:58.382][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:08:58.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.386][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:08:58.387][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:08:58.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.391][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:08:58.392][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:08:58.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.395][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:08:58.397][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:08:58.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.399][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[2024-10-16 22:08:58.400][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:08:58.402][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:08:58.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.405][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:08:58.406][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:08:58.410][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:08:58.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.414][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:08:58.415][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:08:58.416][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:08:58.417][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.423][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:08:58.461][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.485][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:08:58.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.493][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:08:58.494][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.496][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.497][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.498][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.499][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:08:58.500][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:08:58.501][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.502][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:08:58.503][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:08:58.504][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.505][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.507][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:08:58.507][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:08:58.507][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:08:58.507][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:08:58.507][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:08:58.508][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:08:58.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.510][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.511][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:08:58.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.513][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.514][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.515][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.516][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:08:58.517][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:08:58.518][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.519][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.520][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:08:58.523][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.524][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:08:58.525][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.526][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:08:58.527][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.529][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.530][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.531][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:08:58.532][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:08:58.533][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.534][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:08:58.535][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:08:58.536][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.537][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.538][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:08:58.538][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:08:58.538][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:08:58.538][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:08:58.538][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:08:58.540][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:08:58.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.542][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:08:58.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.544][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.545][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.546][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.547][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:08:58.548][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:08:58.549][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.550][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.551][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:08:58.553][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.554][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:08:58.555][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.556][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:08:58.557][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.558][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.559][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.560][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.561][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:08:58.562][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:08:58.563][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.564][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:08:58.565][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:08:58.566][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.567][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.568][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.569][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:08:58.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.571][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.572][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:08:58.573][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.574][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.576][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.577][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:08:58.578][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:08:58.579][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.580][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.581][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:08:58.583][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.584][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:08:58.585][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.586][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:08:58.587][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.588][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.589][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.590][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.591][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:08:58.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:08:58.593][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.594][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:08:58.595][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:08:58.596][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.597][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.598][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.599][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:08:58.600][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.602][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:08:58.603][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.604][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.605][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.606][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.607][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:08:58.608][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:08:58.609][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.610][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:08:58.615][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:08:58.615][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.648][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[2024-10-16 22:08:58.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.694][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:08:58.699][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:08:58.701][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:08:58.702][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:08:58.704][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:08:58.705][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:08:58.707][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:08:58.708][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:08:58.709][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:08:58.711][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:08:58.712][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:08:58.713][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:08:58.715][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:08:58.716][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:08:58.718][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:08:58.719][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:08:58.720][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:08:58.722][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:08:58.723][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:08:58.725][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:08:58.726][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:08:58.727][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:08:58.729][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:08:58.730][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:08:58.732][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:08:58.733][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:08:58.734][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:08:58.736][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:08:58.737][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:08:58.738][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:08:58.740][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:08:58.741][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:08:58.743][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:08:58.744][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:08:58.745][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:08:58.747][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:08:58.748][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:08:58.759][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:08:58.761][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:08:58.762][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:08:58.764][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:08:58.765][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:08:58.766][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:08:58.768][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:08:58.769][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:08:58.770][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:08:58.771][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:08:58.773][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:08:58.774][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:08:58.775][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:08:58.777][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:08:58.778][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:08:58.779][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:08:58.780][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:08:58.782][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:08:58.783][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:08:58.784][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:08:58.785][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:08:58.787][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:08:58.788][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:08:58.789][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:08:58.791][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:08:58.792][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:08:58.793][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:08:58.794][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:08:58.796][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:08:58.797][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:08:58.798][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:08:58.799][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:08:58.801][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:08:58.802][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:08:58.803][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:08:58.805][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:08:58.806][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:08:58.807][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:08:58.808][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:08:58.810][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:08:58.811][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:08:58.812][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:08:58.814][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:08:58.815][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:08:58.816][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:08:58.818][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:08:58.823][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:08:58.825][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:08:58.828][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:08:58.829][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.831][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.847][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.DEBUG[2024-10-16 22:08:58.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.858][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[2024-10-16 22:08:58.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.872][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.875][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[2024-10-16 22:08:58.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.893][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[2024-10-16 22:08:58.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.910][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.DEBUG[2024-10-16 22:08:58.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.922][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[2024-10-16 22:08:58.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:08:58.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:58.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:58.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:58.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:58.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:58.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:08:58.935][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-16 22:08:58.944][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-16 22:08:58.947][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.948][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.949][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:08:58.950][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.951][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.952][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.953][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-16 22:08:58.954][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-16 22:08:58.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:08:58.956][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.957][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-16 22:08:58.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-16 22:08:58.959][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-16 22:08:58.960][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:08:58.961][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:08:58.961][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:08:58.961][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:08:58.962][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-16 22:08:58.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:08:58.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:08:58.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:08:58.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:08:58.968][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:08:58.968][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-16 22:08:58.969][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:08:58.970][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:08:58.971][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:08:58.972][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-16 22:08:58.972][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-16 22:08:58.977][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:08:58.979][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:08:58.980][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-16 22:08:58.982][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:08:58.983][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:08:58.985][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:08:59.012][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-16 22:08:59.013][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-16 22:08:59.018][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-16 22:08:59.022][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-16 22:08:59.026][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:08:59.027][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:08:59.028][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-16 22:08:59.029][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-16 22:08:59.039][biodb::testThat]
biodb.INFO [2024-10-16 22:08:59.040][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-10-16 22:08:59.041][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:08:59.042][biodb::testThat]
biodb.TRACE[2024-10-16 22:08:59.047][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[2024-10-16 22:08:59.049][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:08:59.052][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:08:59.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:08:59.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:59.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:59.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:59.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:59.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:59.078][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.TRACE[2024-10-16 22:08:59.088][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.089][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.091][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.107][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.108][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.110][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.135][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.139][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.140][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.142][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.143][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.147][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.148][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.149][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.151][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.154][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.155][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.157][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.162][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.163][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.165][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.166][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.171][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:08:59.172][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.174][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.175][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:08:59.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.180][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.181][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.182][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.187][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:08:59.188][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:08:59.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.190][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:08:59.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:08:59.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.196][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:08:59.197][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.199][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.200][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:08:59.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.204][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:08:59.205][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:08:59.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.207][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.208][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:08:59.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:08:59.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:08:59.290][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-10-16 22:08:59.293][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.341][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:08:59.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:08:59.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.344][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:08:59.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:08:59.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.348][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 22:08:59.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 22:08:59.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.352][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 22:08:59.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 22:08:59.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.454][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.455][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.457][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.507][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.510][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:08:59.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:08:59.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:08:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:08:59.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:08:59.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:08:59.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:08:59.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.534][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:08:59.535][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:08:59.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.537][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:08:59.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:08:59.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.552][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.557][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.561][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.565][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.566][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.568][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.591][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.592][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.594][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.617][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.618][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.620][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.632][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.636][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.640][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.643][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.644][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.646][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.647][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.658][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.663][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.666][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.670][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.671][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.673][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.674][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.688][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.692][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.696][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.697][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.698][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.699][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.710][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:08:59.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:08:59.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.714][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:08:59.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:08:59.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.723][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:08:59.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:08:59.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.726][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:08:59.727][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:08:59.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.729][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.730][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:08:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:08:59.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.753][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.754][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.756][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.781][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.782][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.784][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.796][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.797][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.799][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.803][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.804][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.806][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.810][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.811][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.813][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.817][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:08:59.818][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:08:59.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.820][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.825][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.826][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:08:59.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.828][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.832][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.833][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:08:59.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.835][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.840][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.841][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:08:59.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.843][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.847][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.848][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:08:59.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.850][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.854][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.855][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:08:59.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.857][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.861][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:08:59.862][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:08:59.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.864][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.868][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:08:59.869][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:08:59.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.871][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 22:08:59.878][biodb::testThat]
biodb.INFO [2024-10-16 22:08:59.879][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-16 22:08:59.880][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:08:59.881][biodb::testThat]
biodb.DEBUG[2024-10-16 22:08:59.898][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-10-16 22:08:59.906][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:08:59.911][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-10-16 22:08:59.913][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:08:59.914][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-10-16 22:08:59.915][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:08:59.938][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:08:59.944][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:08:59.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:08:59.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:08:59.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:08:59.952][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:08:59.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:08:59.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:08:59.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:08:59.956][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.957][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.959][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:08:59.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:08:59.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.981][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.982][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.984][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.985][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:08:59.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:08:59.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.990][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.991][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.993][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:08:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:08:59.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:08:59.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:08:59.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.000][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:00.001][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:00.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.003][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:00.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:00.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.008][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:00.009][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:00.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.011][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:00.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:00.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.016][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:00.017][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:00.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.019][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.020][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:00.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:00.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.024][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:00.025][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:00.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.027][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.028][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:00.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:00.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:00.033][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:00.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.035][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:00.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:00.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.040][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:00.041][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:00.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.043][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:00.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:00.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.049][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:00.050][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:00.050][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.051][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.053][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:00.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:00.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.057][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:00.058][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:00.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.059][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.061][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:00.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:00.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:00.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:00.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:00.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:00.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:00.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:00.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:00.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:00.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:00.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:00.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:00.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:00.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:00.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:00.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:00.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:00.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:00.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:00.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:00.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:00.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:00.106][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-10-16 22:09:00.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-16 22:09:00.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-16 22:09:00.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-16 22:09:00.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-16 22:09:00.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.115][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-16 22:09:00.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-16 22:09:00.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:00.126][biodb::testThat]
biodb.INFO [2024-10-16 22:09:00.128][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-16 22:09:00.129][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:00.130][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:00.133][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:00.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:00.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.136][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:00.137][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-10-16 22:09:00.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:00.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:00.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:00.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:00.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:00.176][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:00.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:00.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:00.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:00.183][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-10-16 22:09:00.188][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-16 22:09:00.208][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:00.226][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-16 22:09:00.228][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:00.229][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-16 22:09:00.251][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:00.254][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:00.255][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:00.256][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:00.957][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:01.576][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:01.579][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-10-16 22:09:01.595][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-10-16 22:09:01.597][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-10-16 22:09:01.609][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:01.610][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:01.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.612][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.613][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.615][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.616][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:01.621][biodb::testThat]
biodb.INFO [2024-10-16 22:09:01.622][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-10-16 22:09:01.623][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:01.624][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:01.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:01.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:01.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:01.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:01.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:01.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:01.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:01.721][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:01.725][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:01.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-16 22:09:01.728][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:01.729][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-10-16 22:09:01.745][biodb::testThat]
biodb.INFO [2024-10-16 22:09:01.746][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-10-16 22:09:01.748][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:01.749][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:01.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:01.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:01.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:01.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:01.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:01.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:01.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.798][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:01.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:01.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.810][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:01.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:01.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.815][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:01.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:01.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:01.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:01.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.823][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:01.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:01.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:01.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:01.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.850][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:01.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:01.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:01.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:01.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:01.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:01.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:01.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.874][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:01.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:01.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.878][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-16 22:09:01.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-16 22:09:01.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.882][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:01.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-16 22:09:01.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:01.887][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:01.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-16 22:09:01.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:01.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:01.897][biodb::testThat]
biodb.INFO [2024-10-16 22:09:01.898][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-16 22:09:01.899][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:01.900][biodb::testThat]
biodb.INFO [2024-10-16 22:09:01.910][biodb::testThat]
biodb.INFO [2024-10-16 22:09:01.911][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-16 22:09:01.912][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:01.913][biodb::testThat]
biodb.INFO [2024-10-16 22:09:01.922][biodb::testThat]
biodb.INFO [2024-10-16 22:09:01.923][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-16 22:09:01.924][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:01.925][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:01.929][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-10-16 22:09:02.806][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-10-16 22:09:03.986][biodb::testThat]
biodb.INFO [2024-10-16 22:09:03.989][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-16 22:09:03.991][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:03.992][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:04.434][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-10-16 22:09:04.905][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:04.907][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:04.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:04.909][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:04.910][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:04.911][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:04.912][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:04.913][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:04.915][biodb::testThat]
biodb.INFO [2024-10-16 22:09:04.916][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-10-16 22:09:04.933][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:04.934][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:04.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:04.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:04.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:04.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:04.957][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:04.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:04.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:04.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:04.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:04.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:04.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:04.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:05.089][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:05.094][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:05.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-16 22:09:05.098][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:05.100][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-16 22:09:05.228][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:05.232][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:05.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-16 22:09:05.235][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:05.237][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-10-16 22:09:05.255][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:05.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:05.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:05.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:05.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:05.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:05.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:05.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:05.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:05.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:05.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:05.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:05.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:05.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:05.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:05.291][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:05.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:05.310][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:05.328][private$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[2024-10-16 22:09:05.747][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[2024-10-16 22:09:06.158][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:06.160][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-10-16 22:09:06.164][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-10-16 22:09:06.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:06.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:06.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:06.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:06.175][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:06.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:06.177][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.DEBUG[2024-10-16 22:09:06.178][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-10-16 22:09:06.241][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:06.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-10-16 22:09:06.245][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:06.246][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:06.247][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:06.248][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:06.249][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:06.250][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:06.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:06.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:06.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:06.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:06.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:06.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:06.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:06.263][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-10-16 22:09:06.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:06.267][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:06.268][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-10-16 22:09:06.675][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-10-16 22:09:07.095][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:07.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-10-16 22:09:07.102][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-10-16 22:09:07.105][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-10-16 22:09:07.107][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:07.109][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:07.111][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:07.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:07.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:07.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:07.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:07.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:07.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:07.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:07.125][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.126][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.128][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.134][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:07.135][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:07.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.137][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.138][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:07.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:07.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.142][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:07.143][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:07.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.145][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.147][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:07.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:07.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.151][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:07.152][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:07.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.154][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:07.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:07.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.160][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:07.161][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:07.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.163][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.164][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:07.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:07.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.168][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:07.169][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:07.170][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.171][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.173][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:07.174][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:07.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.176][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.178][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:07.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:07.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:07.183][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:07.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.185][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:07.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:07.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.191][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:07.192][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:07.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.194][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:07.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:07.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.199][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:07.200][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:07.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.202][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.203][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:07.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:07.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.208][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:07.209][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:07.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.211][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.212][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:07.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:07.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:07.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:07.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:07.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:07.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:07.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:07.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:07.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:07.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:07.267][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-10-16 22:09:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:07.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:07.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:07.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:07.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:07.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:07.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:07.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:07.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:07.293][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:07.297][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:07.298][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:07.300][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:07.714][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:08.118][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:08.120][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-10-16 22:09:08.126][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-10-16 22:09:08.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:08.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:08.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:08.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:08.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:08.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:08.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:08.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:08.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:08.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:08.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:08.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:08.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:08.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:08.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:08.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:08.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:08.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:08.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:08.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:08.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:08.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:08.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:08.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:08.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:08.175][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-10-16 22:09:08.176][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:08.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-10-16 22:09:08.179][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:08.180][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:08.181][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:08.182][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:08.183][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:08.184][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:08.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:08.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:08.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:08.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:08.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:08.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:08.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:08.208][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-10-16 22:09:08.210][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:08.211][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:08.212][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-10-16 22:09:08.620][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-10-16 22:09:09.046][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:09.055][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-10-16 22:09:09.062][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-10-16 22:09:09.066][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-10-16 22:09:09.068][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:09.070][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:09.072][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:09.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:09.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:09.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:09.091][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:09.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:09.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:09.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:09.101][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.164][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.185][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:09.187][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:09.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.190][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.193][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:09.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:09.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.198][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:09.200][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:09.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.203][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.205][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:09.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:09.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.211][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:09.212][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:09.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.215][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:09.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:09.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.222][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:09.224][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:09.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.226][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:09.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:09.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.233][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:09.234][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:09.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.237][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.239][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:09.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.244][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.246][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:09.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.252][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:09.254][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:09.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.256][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:09.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:09.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.263][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:09.264][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:09.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.267][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.269][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:09.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:09.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.274][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:09.276][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:09.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.279][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.280][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:09.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:09.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.286][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:09.287][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:09.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.289][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.291][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:09.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:09.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:09.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.302][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:09.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:09.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:09.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:09.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:09.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:09.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:09.350][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-10-16 22:09:09.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:09.389][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:09.393][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:09.394][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-16 22:09:09.396][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:09.397][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-16 22:09:09.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:09.401][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:09.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:09.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:09.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:09.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:09.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:09.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:09.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:09.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:09.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:09.427][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:09.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:09.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:09.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:09.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:09.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:09.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:09.437][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-10-16 22:09:09.438][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:09.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-10-16 22:09:09.441][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:09.442][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:09.443][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:09.444][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:09.445][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:09.446][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:09.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:09.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:09.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:09.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:09.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:09.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:09.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:09.458][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-10-16 22:09:09.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:09.462][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:09.463][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-10-16 22:09:10.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-10-16 22:09:10.523][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:10.525][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-10-16 22:09:10.528][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-10-16 22:09:10.531][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-10-16 22:09:10.532][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:10.534][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:10.535][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:10.537][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:10.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:10.538][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:10.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.544][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:10.548][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.549][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.550][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.556][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:10.557][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:10.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.559][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.560][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:10.562][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:10.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.564][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.565][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:10.567][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:10.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.569][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.570][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:10.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:10.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.573][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.574][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:10.575][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:10.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.577][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.578][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:10.579][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.581][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.582][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:10.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:10.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.585][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.586][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:10.587][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:10.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.589][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:10.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:10.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.594][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:10.596][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:10.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.597][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.599][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:10.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:10.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.603][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:10.604][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:10.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.605][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:10.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:10.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:10.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:10.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:10.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:10.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:10.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:10.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:10.654][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-10-16 22:09:10.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:10.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:10.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:10.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:10.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:10.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:10.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:10.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.687][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-10-16 22:09:10.688][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:10.689][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-10-16 22:09:10.691][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:10.692][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:10.693][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:10.694][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:10.695][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:10.696][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:10.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:10.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:10.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:10.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:10.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:10.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:10.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:10.708][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-10-16 22:09:10.711][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:10.712][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:10.714][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-10-16 22:09:11.118][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-10-16 22:09:11.526][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:11.529][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-10-16 22:09:11.532][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-10-16 22:09:11.534][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-10-16 22:09:11.535][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:11.537][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:11.538][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:11.539][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:11.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:11.550][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.551][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.553][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.554][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.558][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:11.559][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:11.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.561][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.562][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:11.563][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:11.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.565][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.566][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:11.567][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:11.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.569][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.570][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:11.571][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:11.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.573][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.574][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:11.575][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:11.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.577][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.579][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:11.580][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.582][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.583][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:11.584][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:11.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.586][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.587][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:11.588][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:11.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.590][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:11.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:11.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.595][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:11.597][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:11.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.598][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.600][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:11.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:11.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.604][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:11.605][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:11.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.608][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:11.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:11.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:11.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:11.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:11.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:11.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:11.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:11.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:11.657][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-10-16 22:09:11.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.662][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:11.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:11.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:11.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:11.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:11.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.688][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-10-16 22:09:11.689][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:11.690][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-10-16 22:09:11.692][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:11.693][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:11.694][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:11.695][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:11.696][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:11.696][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:11.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:11.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:11.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:11.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:11.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:11.716][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:11.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:11.718][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-10-16 22:09:11.722][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:11.723][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:11.725][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-10-16 22:09:12.129][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-10-16 22:09:12.533][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:12.536][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-10-16 22:09:12.540][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-10-16 22:09:12.544][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-10-16 22:09:12.546][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:12.547][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:12.548][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:12.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:12.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:12.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:12.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:12.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:12.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:12.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:12.564][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.565][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.567][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.573][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:12.574][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:12.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.576][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.577][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:12.579][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:12.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.582][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.584][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:12.585][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:12.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.587][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.589][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:12.590][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:12.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.592][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.593][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:12.595][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:12.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.597][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.598][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:12.599][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.601][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.603][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:12.604][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:12.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.606][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.607][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:12.608][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:12.609][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.610][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:12.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:12.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.616][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:12.617][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:12.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.619][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.621][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:12.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:12.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.625][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:12.626][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:12.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.628][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:12.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:12.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:12.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:12.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:12.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:12.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.681][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:12.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:12.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:12.690][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-10-16 22:09:12.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:12.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:12.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:12.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:12.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:12.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:12.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:12.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:12.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:12.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:12.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:12.722][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-10-16 22:09:12.723][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:12.725][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-10-16 22:09:12.726][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:12.727][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:12.728][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:12.729][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:12.730][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:12.731][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:12.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:12.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:12.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:12.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:12.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:12.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:12.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:12.744][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-10-16 22:09:12.746][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:12.747][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:12.749][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-10-16 22:09:13.155][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-10-16 22:09:13.828][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-10-16 22:09:13.830][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-10-16 22:09:13.831][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-10-16 22:09:13.834][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-10-16 22:09:13.837][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-10-16 22:09:13.838][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:13.839][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:13.840][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:13.842][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:13.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:13.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:13.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:13.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:13.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:13.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:13.853][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.854][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.856][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.861][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:13.862][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:13.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.864][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.865][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:13.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:13.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.869][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:13.870][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:13.871][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.872][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.873][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:13.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:13.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.877][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:13.878][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:13.879][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.880][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:13.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:13.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.885][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.886][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.888][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:13.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.893][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.894][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.896][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.897][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:13.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.901][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:13.902][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:13.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.904][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.905][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:13.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:13.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.909][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.910][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.912][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:13.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.926][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.927][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.928][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.929][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.931][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:13.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:13.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.935][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:13.936][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:13.936][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.937][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.939][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:13.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:13.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:13.944][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:13.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.945][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.947][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:13.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:13.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:13.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:13.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:13.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:13.990][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-10-16 22:09:13.991][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:13.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:13.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:13.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:13.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:13.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:13.998][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:13.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:14.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:14.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:14.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:14.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.012][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-10-16 22:09:14.013][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:14.015][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-10-16 22:09:14.016][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:14.017][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:14.018][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:14.019][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:14.020][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:14.021][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:14.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:14.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:14.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:14.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:14.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:14.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:14.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:14.034][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-10-16 22:09:14.037][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:14.038][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:14.039][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-10-16 22:09:15.499][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-10-16 22:09:15.903][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-10-16 22:09:15.905][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-10-16 22:09:15.907][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-10-16 22:09:15.910][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-10-16 22:09:15.912][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-10-16 22:09:15.914][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:15.915][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:15.916][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:15.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:15.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:15.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:15.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:15.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:15.925][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:15.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:15.928][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.929][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.931][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:15.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:15.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.936][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:15.937][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:15.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.939][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.940][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:15.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:15.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.944][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:15.945][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:15.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.947][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.948][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:15.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:15.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.961][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:15.962][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:15.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.964][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:15.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:15.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.969][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.970][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.972][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.973][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:15.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.977][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.978][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.980][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.981][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:15.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.985][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:15.986][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:15.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.987][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.989][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:15.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:15.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.993][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.994][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.995][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:15.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:15.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:15.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.000][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:16.001][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:16.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.003][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:16.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:16.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.008][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:16.009][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:16.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.011][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.012][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:16.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:16.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.016][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:16.017][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:16.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.019][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.020][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:16.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:16.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:16.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:16.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:16.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:16.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:16.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:16.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:16.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:16.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:16.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:16.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:16.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:16.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:16.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:16.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:16.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:16.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:16.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:16.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:16.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:16.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:16.062][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-10-16 22:09:16.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:16.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:16.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:16.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:16.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:16.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:16.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:16.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:16.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:16.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:16.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:16.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:16.080][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:16.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:16.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:16.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:16.083][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-10-16 22:09:16.084][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:16.086][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-10-16 22:09:16.087][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:16.088][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:16.089][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:16.090][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:16.091][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:16.092][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:16.095][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:16.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:16.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:16.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:16.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:16.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:16.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:16.104][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-10-16 22:09:16.107][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:16.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:16.109][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-10-16 22:09:16.514][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-10-16 22:09:17.148][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:17.151][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-10-16 22:09:17.157][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-10-16 22:09:17.162][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-10-16 22:09:17.164][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:17.167][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:17.169][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:17.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:17.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:17.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:17.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:17.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:17.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:17.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:17.212][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.213][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.216][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.224][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:17.225][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:17.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.227][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.229][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:17.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.233][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:17.234][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:17.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.236][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:17.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:17.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.242][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:17.243][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:17.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.245][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:17.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:17.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.250][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:17.251][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:17.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.253][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:17.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:17.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.259][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:17.260][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:17.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.262][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.263][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:17.265][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:17.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.266][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.268][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:17.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:17.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.272][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:17.273][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:17.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.275][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:17.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:17.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.281][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:17.282][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:17.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.284][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:17.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:17.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.289][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:17.290][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:17.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.292][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.294][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:17.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:17.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.298][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:17.299][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:17.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.301][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.302][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:17.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:17.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:17.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:17.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:17.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:17.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:17.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:17.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:17.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:17.348][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-10-16 22:09:17.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:17.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:17.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:17.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:17.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:17.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:17.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:17.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:17.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:17.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:17.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:17.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:17.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:17.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:17.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:17.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:17.372][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-10-16 22:09:17.373][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:17.375][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-10-16 22:09:17.376][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:17.377][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:17.378][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:17.379][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:17.380][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:17.393][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:17.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:17.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:17.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:17.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:17.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:17.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:17.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:17.406][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-10-16 22:09:17.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:17.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:17.411][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-10-16 22:09:17.819][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-10-16 22:09:18.479][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:18.483][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-10-16 22:09:18.488][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-10-16 22:09:18.491][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-10-16 22:09:18.492][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:18.493][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:18.494][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:18.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:18.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:18.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:18.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:18.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:18.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:18.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:18.507][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.508][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.510][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.515][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:18.516][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:18.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.518][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.519][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:18.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:18.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.523][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:18.524][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:18.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.526][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:18.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:18.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.531][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:18.532][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:18.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.533][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:18.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:18.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.539][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:18.540][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:18.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.542][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:18.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:18.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.547][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:18.548][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:18.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.549][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.551][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:18.552][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:18.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.553][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.555][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:18.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:18.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.558][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:18.559][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:18.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.561][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:18.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:18.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.566][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:18.567][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:18.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.569][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:18.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.574][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:18.575][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:18.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.577][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.578][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:18.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.582][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:18.583][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:18.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.585][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.586][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:18.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:18.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:18.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:18.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:18.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:18.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:18.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:18.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:18.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:18.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:18.637][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-10-16 22:09:18.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:18.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:18.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:18.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:18.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:18.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:18.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:18.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:18.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:18.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:18.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:18.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:18.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:18.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:18.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:18.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:18.666][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-10-16 22:09:18.667][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:18.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-10-16 22:09:18.672][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:18.673][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:18.675][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:18.676][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:18.677][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:18.678][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:18.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:18.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:18.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:18.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:18.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:18.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:18.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:18.690][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-10-16 22:09:18.693][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:18.694][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:18.695][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-10-16 22:09:19.098][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-10-16 22:09:19.540][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:19.545][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-10-16 22:09:19.553][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-10-16 22:09:19.557][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-10-16 22:09:19.560][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:19.562][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:19.564][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:19.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:19.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:19.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:19.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:19.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:19.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:19.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:19.586][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.588][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.591][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.598][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:19.600][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:19.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.603][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.604][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:19.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:19.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.609][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:19.610][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:19.611][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.612][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:19.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:19.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.618][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:19.619][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:19.620][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.621][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.622][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:19.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:19.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.626][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:19.627][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:19.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.629][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:19.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:19.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.634][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:19.635][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:19.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.637][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.638][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:19.639][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:19.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.641][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.642][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:19.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:19.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.646][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:19.647][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:19.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.648][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:19.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:19.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.654][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:19.655][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:19.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.657][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:19.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:19.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.662][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:19.663][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:19.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.665][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.666][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:19.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:19.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.670][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:19.671][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:19.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.673][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.674][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:19.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:19.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:19.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:19.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:19.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:19.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:19.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:19.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:19.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:19.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:19.724][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-10-16 22:09:19.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:19.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:19.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:19.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:19.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:19.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:19.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:19.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:19.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:19.736][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:19.737][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:19.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:19.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:19.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:19.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:19.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:19.746][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-10-16 22:09:19.747][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:19.749][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-10-16 22:09:19.750][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:19.751][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:19.752][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:19.753][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:19.754][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:19.755][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:19.757][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:19.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:19.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:19.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:19.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:19.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:19.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:19.767][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-10-16 22:09:19.770][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:19.771][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:19.772][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-10-16 22:09:20.174][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-10-16 22:09:20.612][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:20.615][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-10-16 22:09:20.621][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-10-16 22:09:20.627][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-10-16 22:09:20.630][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:20.633][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:20.635][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:20.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:20.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:20.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:20.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:20.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:20.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:20.656][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[2024-10-16 22:09:20.660][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.662][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.663][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.665][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.673][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:20.674][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:20.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.676][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.678][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:20.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.683][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:20.684][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:20.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.686][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:20.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:20.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.692][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:20.693][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:20.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.695][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:20.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:20.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.700][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:20.701][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:20.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.703][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:20.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:20.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.708][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:20.709][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:20.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.711][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.712][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:20.713][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:20.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.715][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.716][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:20.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:20.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.720][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:20.721][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:20.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.722][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:20.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:20.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.767][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:20.768][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:20.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.770][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:20.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:20.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:20.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:20.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.778][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.779][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:20.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:20.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:20.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:20.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.786][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.787][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:20.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:20.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:20.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:20.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:20.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:20.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:20.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:20.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:20.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:20.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:20.829][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-10-16 22:09:20.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:20.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:20.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:20.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:20.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:20.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:20.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:20.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:20.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:20.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:20.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:20.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:20.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:20.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:20.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:20.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:20.850][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-10-16 22:09:20.851][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:20.852][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-10-16 22:09:20.854][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:20.855][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:20.856][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:20.857][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:20.858][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:20.858][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:20.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:20.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:20.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:20.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:20.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:20.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:20.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:20.870][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-10-16 22:09:20.873][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:20.874][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:20.875][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-10-16 22:09:21.276][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-10-16 22:09:21.912][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:21.916][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-10-16 22:09:21.924][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-10-16 22:09:21.930][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-10-16 22:09:21.933][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:21.936][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:21.938][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:21.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:21.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:21.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:21.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:21.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:21.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:21.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:21.965][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:21.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:21.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:21.970][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:21.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:21.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:21.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:21.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:21.978][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:21.980][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:21.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:21.982][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:21.984][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:21.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:21.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:21.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:21.989][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:21.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:21.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:21.993][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:21.994][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:21.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:21.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:21.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:21.998][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:22.000][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:22.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.002][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:22.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:22.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.019][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:22.020][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:22.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.022][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:22.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:22.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.027][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:22.028][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:22.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.030][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.031][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:22.032][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:22.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.034][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.035][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:22.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:22.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.039][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:22.040][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:22.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.042][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:22.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:22.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.047][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:22.048][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:22.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.050][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:22.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:22.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.061][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:22.062][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:22.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.064][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.065][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:22.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:22.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.070][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:22.071][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:22.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.073][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.074][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:22.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:22.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:22.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:22.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:22.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:22.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:22.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:22.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:22.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:22.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:22.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:22.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:22.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:22.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:22.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:22.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:22.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:22.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:22.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:22.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:22.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:22.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:22.121][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-10-16 22:09:22.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:22.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:22.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:22.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:22.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:22.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:22.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:22.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:22.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:22.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:22.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:22.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:22.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:22.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:22.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:22.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:22.148][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-10-16 22:09:22.149][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:22.151][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-10-16 22:09:22.152][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:22.154][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:22.155][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:22.156][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:22.157][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:22.158][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:22.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:22.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:22.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:22.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:22.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:22.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:22.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:22.172][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-10-16 22:09:22.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:22.176][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:22.178][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-10-16 22:09:22.589][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-10-16 22:09:23.031][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:23.036][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-10-16 22:09:23.044][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-10-16 22:09:23.050][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-10-16 22:09:23.054][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:23.057][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:23.059][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:23.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:23.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:23.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:23.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:23.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:23.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:23.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:23.108][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.109][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.112][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.118][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:23.119][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:23.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.121][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.123][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:23.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:23.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.127][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:23.128][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:23.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.130][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.132][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:23.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:23.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.136][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:23.137][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:23.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.139][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.140][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:23.141][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:23.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.143][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.144][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:23.145][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:23.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.147][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.148][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:23.149][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:23.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.151][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.152][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:23.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:23.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.156][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:23.157][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:23.158][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.159][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:23.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:23.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.164][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:23.165][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:23.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.167][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:23.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:23.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.172][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:23.173][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:23.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.175][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.176][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:23.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:23.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.180][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:23.181][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:23.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.182][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:23.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:23.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:23.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:23.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:23.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:23.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:23.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:23.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:23.222][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-10-16 22:09:23.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:23.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:23.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:23.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:23.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:23.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:23.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:23.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:23.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:23.235][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:23.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:23.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:23.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:23.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:23.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:23.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:23.245][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-10-16 22:09:23.246][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:23.247][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-10-16 22:09:23.248][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:23.249][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:23.251][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:23.252][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:23.253][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:23.253][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:23.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:23.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:23.258][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:23.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:23.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:23.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:23.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:23.266][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-10-16 22:09:23.269][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:23.270][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:23.271][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-10-16 22:09:23.680][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-10-16 22:09:24.133][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:24.136][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-10-16 22:09:24.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-10-16 22:09:24.152][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-10-16 22:09:24.154][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:24.155][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:24.156][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:24.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:24.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:24.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:24.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:24.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:24.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:24.170][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.171][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.173][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.179][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:24.180][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:24.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.182][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.183][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:24.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:24.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.187][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:24.188][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:24.189][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.190][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.191][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:24.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:24.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.195][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:24.196][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:24.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.198][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.199][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:24.200][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:24.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.202][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.203][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:24.204][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:24.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.206][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.207][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:24.208][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:24.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.210][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.211][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:24.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:24.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.215][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:24.216][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:24.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.218][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:24.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:24.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.223][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:24.224][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:24.225][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:24.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:24.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.231][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:24.232][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:24.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.234][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.235][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:24.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:24.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.239][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:24.240][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:24.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.241][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:24.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:24.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:24.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:24.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:24.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:24.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:24.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:24.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:24.281][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-10-16 22:09:24.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:24.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:24.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:24.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:24.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:24.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:24.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:24.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:24.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:24.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:24.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:24.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:24.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:24.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.302][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-10-16 22:09:24.303][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:24.305][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-10-16 22:09:24.306][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:24.307][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:24.308][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:24.309][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:24.310][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:24.311][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:24.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:24.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:24.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:24.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:24.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:24.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:24.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:24.329][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-10-16 22:09:24.331][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:24.332][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:24.334][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-10-16 22:09:24.736][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-10-16 22:09:25.153][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:25.159][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-10-16 22:09:25.166][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-10-16 22:09:25.170][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-10-16 22:09:25.173][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:25.174][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:25.176][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:25.178][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:25.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:25.192][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.193][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.195][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.201][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:25.202][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:25.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.204][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.205][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:25.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:25.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.210][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.211][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.213][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:25.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:25.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.218][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:25.219][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:25.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.221][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.223][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:25.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:25.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.227][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:25.228][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:25.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.230][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:25.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:25.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.235][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:25.236][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:25.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.238][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.240][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:25.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:25.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.244][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:25.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:25.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.248][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.249][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.251][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:25.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.256][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.258][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.259][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:25.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:25.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.265][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:25.266][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:25.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.268][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.270][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:25.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:25.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.274][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:25.275][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:25.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.277][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.278][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:25.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:25.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:25.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:25.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:25.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:25.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:25.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:25.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:25.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:25.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:25.323][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-10-16 22:09:25.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:25.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:25.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:25.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:25.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:25.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:25.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:25.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:25.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:25.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:25.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.362][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-10-16 22:09:25.363][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:25.364][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-10-16 22:09:25.365][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:25.367][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:25.368][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:25.369][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:25.369][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:25.370][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:25.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:25.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:25.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:25.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:25.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:25.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:25.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:25.383][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-10-16 22:09:25.385][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:25.386][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:25.388][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-10-16 22:09:25.793][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-10-16 22:09:26.230][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:26.234][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-10-16 22:09:26.239][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-10-16 22:09:26.243][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-10-16 22:09:26.246][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:26.248][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:26.249][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:26.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:26.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:26.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:26.262][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:26.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:26.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:26.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:26.269][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.271][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.274][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.282][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:26.283][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:26.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.286][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.288][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:26.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:26.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.294][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:26.296][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:26.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.298][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.300][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:26.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:26.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.307][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:26.308][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:26.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.311][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.313][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:26.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:26.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.319][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:26.320][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:26.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.323][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:26.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:26.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.331][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:26.333][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:26.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.335][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.337][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:26.339][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:26.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.341][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.342][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:26.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:26.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.346][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:26.347][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:26.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.349][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:26.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:26.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.354][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.355][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.357][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.358][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:26.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:26.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.362][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:26.363][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:26.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.365][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.366][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:26.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:26.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.370][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:26.371][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:26.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.373][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.374][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:26.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:26.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:26.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:26.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:26.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:26.425][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-10-16 22:09:26.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:26.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:26.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:26.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:26.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:26.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:26.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:26.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:26.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:26.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:26.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:26.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:26.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:26.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:26.445][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:26.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:26.447][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-10-16 22:09:26.448][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:26.449][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-10-16 22:09:26.450][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:26.452][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:26.453][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:26.454][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:26.454][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:26.455][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:26.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:26.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:26.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:26.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:26.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:26.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:26.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:26.468][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-10-16 22:09:26.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:26.471][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:26.472][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-10-16 22:09:26.876][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-10-16 22:09:27.546][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:27.551][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-10-16 22:09:27.558][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-10-16 22:09:27.564][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-10-16 22:09:27.567][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:27.570][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:27.573][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:27.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:27.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:27.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:27.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:27.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:27.593][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:27.595][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[2024-10-16 22:09:27.599][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.601][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.604][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.612][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:27.613][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:27.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.616][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:27.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:27.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.623][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:27.624][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:27.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.626][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.628][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:27.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:27.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.632][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:27.633][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:27.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.635][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:27.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:27.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.641][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:27.642][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:27.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.643][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:27.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:27.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.649][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:27.650][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:27.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.651][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.653][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:27.654][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:27.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.655][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.657][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:27.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:27.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.661][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:27.662][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:27.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.663][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:27.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:27.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.669][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:27.670][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:27.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.672][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:27.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:27.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.686][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:27.687][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:27.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.689][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.690][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:27.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:27.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.694][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:27.695][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:27.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.696][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.698][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:27.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:27.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:27.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:27.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:27.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:27.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:27.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:27.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:27.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:27.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:27.739][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-10-16 22:09:27.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:27.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:27.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:27.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:27.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:27.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:27.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:27.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:27.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:27.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:27.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:27.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:27.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:27.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:27.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:27.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:27.761][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-10-16 22:09:27.762][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:27.763][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-10-16 22:09:27.765][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:27.766][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:27.767][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:27.768][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:27.769][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:27.770][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:27.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:27.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:27.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:27.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:27.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:27.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:27.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:27.782][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-10-16 22:09:27.784][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:27.785][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:27.786][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-10-16 22:09:28.190][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-10-16 22:09:28.647][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:28.651][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-10-16 22:09:28.656][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-10-16 22:09:28.659][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-10-16 22:09:28.660][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:28.662][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:28.663][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:28.665][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:28.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:28.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:28.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:28.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:28.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:28.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:28.680][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.681][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.683][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.688][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:28.690][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:28.691][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.692][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.693][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:28.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:28.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.697][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:28.698][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:28.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.700][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.701][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:28.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.706][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:28.707][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:28.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.709][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:28.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:28.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.714][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:28.715][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:28.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.717][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:28.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:28.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.745][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:28.746][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:28.747][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.748][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.749][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:28.751][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.753][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.754][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:28.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.758][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.759][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.761][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:28.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.767][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:28.768][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:28.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.770][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:28.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:28.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:28.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:28.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.778][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.780][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:28.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:28.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.784][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:28.785][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:28.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.787][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.788][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:28.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:28.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:28.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:28.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:28.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:28.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:28.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:28.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:28.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:28.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:28.835][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-10-16 22:09:28.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:28.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:28.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:28.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:28.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:28.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:28.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:28.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:28.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:28.862][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-10-16 22:09:28.863][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:28.865][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-10-16 22:09:28.866][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:28.867][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:28.868][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:28.869][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:28.870][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:28.871][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:28.874][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:28.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:28.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:28.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:28.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:28.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:28.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:28.884][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-10-16 22:09:28.887][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:28.888][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:28.889][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-10-16 22:09:29.518][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-10-16 22:09:29.967][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:29.970][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-10-16 22:09:29.974][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-10-16 22:09:29.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-10-16 22:09:29.979][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:29.981][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:29.982][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:29.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:29.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:29.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:29.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:29.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:29.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:29.995][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.TRACE[2024-10-16 22:09:29.998][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:29.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.002][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:30.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.019][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:30.020][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:30.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.022][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.023][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:30.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:30.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.028][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:30.029][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:30.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.031][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:30.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:30.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.036][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:30.037][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:30.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.039][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:30.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:30.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.044][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:30.045][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:30.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.047][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:30.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:30.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.052][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:30.053][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:30.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.055][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.056][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:30.057][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:30.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.059][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.060][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:30.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:30.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.064][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:30.065][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:30.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.066][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:30.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:30.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.071][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:30.072][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:30.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.074][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:30.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:30.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.079][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:30.080][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:30.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.082][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.083][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:30.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:30.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.087][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:30.088][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:30.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.090][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.091][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:30.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:30.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:30.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:30.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:30.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:30.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:30.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:30.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:30.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:30.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:30.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:30.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:30.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:30.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:30.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:30.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:30.133][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-10-16 22:09:30.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:30.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:30.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:30.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:30.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:30.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:30.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:30.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:30.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:30.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:30.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:30.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:30.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:30.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:30.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:30.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:30.154][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-10-16 22:09:30.155][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:30.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-10-16 22:09:30.158][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:30.159][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:30.160][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:30.161][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:30.162][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:30.163][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:30.165][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:30.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:30.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:30.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:30.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:30.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:30.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:30.175][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-10-16 22:09:30.182][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:30.183][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:30.185][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-10-16 22:09:30.821][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-10-16 22:09:31.491][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:31.493][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-10-16 22:09:31.496][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-10-16 22:09:31.498][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-10-16 22:09:31.500][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:31.501][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:31.502][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:31.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:31.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:31.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:31.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:31.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:31.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:31.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:31.515][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.516][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.518][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.523][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:31.524][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:31.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.525][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.527][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:31.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:31.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.531][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:31.532][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:31.533][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.533][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.535][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:31.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:31.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.539][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:31.540][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:31.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.541][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:31.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:31.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.546][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:31.547][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:31.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.549][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:31.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:31.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.554][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:31.555][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:31.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.557][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.558][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:31.559][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:31.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.561][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.562][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:31.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:31.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.566][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:31.570][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:31.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.573][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:31.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:31.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.579][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:31.580][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:31.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.582][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:31.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:31.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.588][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:31.589][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:31.590][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.591][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.592][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:31.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.596][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:31.598][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:31.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.600][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.601][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:31.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:31.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:31.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:31.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:31.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:31.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:31.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:31.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:31.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:31.647][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-10-16 22:09:31.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:31.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:31.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:31.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:31.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:31.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:31.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:31.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:31.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:31.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:31.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:31.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:31.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:31.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:31.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:31.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:31.694][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-10-16 22:09:31.695][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:31.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-10-16 22:09:31.698][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:31.699][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:31.700][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:31.701][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:31.702][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:31.703][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:31.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:31.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:31.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:31.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:31.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:31.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:31.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:31.717][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-10-16 22:09:31.719][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:31.720][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:31.722][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-10-16 22:09:32.133][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-10-16 22:09:32.576][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:32.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-10-16 22:09:32.583][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-10-16 22:09:32.586][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-10-16 22:09:32.587][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:32.589][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:32.590][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:32.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:32.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:32.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:32.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:32.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:32.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:32.601][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.TRACE[2024-10-16 22:09:32.603][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.605][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.606][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.612][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:32.613][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:32.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.615][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.616][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:32.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:32.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.620][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:32.621][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:32.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.623][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.625][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:32.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:32.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.629][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:32.630][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:32.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.631][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:32.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:32.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.636][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:32.637][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:32.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.639][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:32.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:32.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.644][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:32.645][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:32.646][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.647][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.648][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:32.649][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:32.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.651][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.652][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:32.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:32.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.656][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:32.657][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:32.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.659][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:32.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:32.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.664][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:32.665][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:32.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.667][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.668][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:32.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:32.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.672][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:32.673][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:32.674][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.675][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.676][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:32.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:32.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.680][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:32.681][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:32.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.683][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.684][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:32.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:32.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.688][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:32.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:32.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:32.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:32.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:32.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:32.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:32.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:32.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:32.735][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-10-16 22:09:32.736][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:32.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:32.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:32.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:32.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:32.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:32.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:32.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:32.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:32.763][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:32.766][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:32.767][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:32.769][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:33.310][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:33.870][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:33.873][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-10-16 22:09:33.876][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-10-16 22:09:33.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:33.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:33.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:33.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:33.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:33.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:33.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:33.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:33.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:33.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:33.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:33.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:33.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:33.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:33.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:33.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:33.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:33.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:33.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:33.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:33.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:33.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:33.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:33.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:33.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:33.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:33.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:33.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:33.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:33.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:33.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:33.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:33.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:33.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:33.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:33.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:33.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:33.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.005][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.028][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.047][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.048][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.TRACE[2024-10-16 22:09:34.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.060][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.081][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.089][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.090][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.TRACE[2024-10-16 22:09:34.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.103][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.144][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.202][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.276][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.TRACE[2024-10-16 22:09:34.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.324][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[2024-10-16 22:09:34.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.353][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:34.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:34.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:34.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:34.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:34.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:34.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:34.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:34.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:34.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:34.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:34.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:34.439][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:34.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:34.443][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:34.445][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:34.856][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:35.265][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:35.270][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-10-16 22:09:35.278][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-10-16 22:09:35.286][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:35.293][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:35.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:35.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:35.972][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:36.382][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:36.384][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-10-16 22:09:36.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-10-16 22:09:36.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:36.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:36.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:36.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:36.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:36.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:36.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:36.419][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-10-16 22:09:36.421][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:36.424][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-10-16 22:09:36.426][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:36.428][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:36.430][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:36.432][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:36.433][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:36.435][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:36.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:36.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:36.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:36.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:36.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:36.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:36.451][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[2024-10-16 22:09:36.452][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-10-16 22:09:36.456][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:36.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:36.459][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-10-16 22:09:36.870][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-10-16 22:09:37.319][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:37.322][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-10-16 22:09:37.328][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-10-16 22:09:37.349][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-10-16 22:09:37.352][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:37.354][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:37.356][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:37.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:37.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:37.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:37.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:37.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:37.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:37.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:37.374][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.376][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.378][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.384][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:37.385][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:37.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.387][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.389][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:37.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:37.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.393][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:37.394][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:37.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.396][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.397][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:37.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:37.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.402][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:37.403][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:37.404][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.405][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:37.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:37.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.410][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:37.411][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:37.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.413][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:37.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:37.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.419][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:37.420][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:37.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.421][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.423][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:37.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:37.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.426][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:37.427][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:37.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.429][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.431][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:37.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:37.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.434][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.435][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.437][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.442][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:37.443][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:37.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.445][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:37.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:37.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.451][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:37.452][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:37.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.453][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.455][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:37.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:37.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.458][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:37.459][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:37.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.461][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.462][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:37.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:37.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:37.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:37.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:37.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:37.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:37.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:37.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:37.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:37.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:37.505][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-10-16 22:09:37.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:37.517][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:37.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:37.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:37.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:37.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:37.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:37.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:37.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.536][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:37.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:37.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:37.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:37.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:37.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:37.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:37.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:37.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:37.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:37.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:37.553][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-10-16 22:09:37.554][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:37.555][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-10-16 22:09:37.557][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:37.558][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:37.559][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:37.560][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:37.561][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:37.562][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:37.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:37.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:37.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:37.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:37.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:37.572][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:37.573][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[2024-10-16 22:09:37.574][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-10-16 22:09:37.577][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:37.578][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:37.579][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-10-16 22:09:37.982][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-10-16 22:09:38.385][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:38.387][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-10-16 22:09:38.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-10-16 22:09:38.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-10-16 22:09:38.395][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:38.396][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:38.397][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:38.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.410][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.411][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.413][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.418][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:38.419][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:38.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.421][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.422][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:38.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:38.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.426][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:38.427][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:38.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.429][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.430][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:38.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:38.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.434][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:38.435][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:38.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.437][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.438][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:38.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:38.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.442][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:38.443][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:38.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.445][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.446][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:38.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:38.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.450][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:38.451][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:38.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.453][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.454][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:38.455][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:38.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.457][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.458][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:38.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:38.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.462][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.463][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.465][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.470][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:38.471][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:38.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.473][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:38.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:38.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.478][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:38.480][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:38.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.481][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.483][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:38.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:38.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.487][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:38.488][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:38.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.489][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:38.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:38.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:38.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:38.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:38.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:38.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:38.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:38.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.547][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:38.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:38.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.568][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-10-16 22:09:38.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.601][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:38.605][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:38.606][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-16 22:09:38.608][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:38.609][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-16 22:09:38.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.764][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.TRACE[2024-10-16 22:09:38.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.808][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[2024-10-16 22:09:38.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.871][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.937][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:38.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:38.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:38.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:38.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:38.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:38.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:38.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:38.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:38.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:38.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:38.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.072][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.082][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.084][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.085][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[2024-10-16 22:09:39.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.113][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:39.116][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:39.117][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-16 22:09:39.118][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:39.119][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-16 22:09:39.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.151][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.TRACE[2024-10-16 22:09:39.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.196][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.217][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.256][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.360][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.416][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.TRACE[2024-10-16 22:09:39.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.436][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[2024-10-16 22:09:39.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.455][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.499][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.500][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[2024-10-16 22:09:39.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.554][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:39.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:39.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.593][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:39.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:39.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:39.603][biodb::testThat]
biodb.INFO [2024-10-16 22:09:39.604][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-16 22:09:39.605][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:39.606][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:39.608][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:39.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:39.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:39.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:39.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:39.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:39.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:39.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:39.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:39.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:39.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:39.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:39.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:39.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:39.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:39.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:39.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:39.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:39.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:39.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:39.645][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:39.648][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:39.649][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:39.651][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:40.064][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:40.473][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:40.475][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-10-16 22:09:40.479][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-10-16 22:09:40.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:40.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:40.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:40.489][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:40.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:40.490][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:40.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:40.492][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:40.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:40.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:40.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:40.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:40.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:40.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:40.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:40.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:40.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:40.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:40.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:40.505][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:40.509][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:40.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:40.511][private$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[2024-10-16 22:09:40.914][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[2024-10-16 22:09:41.359][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:41.361][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-10-16 22:09:41.365][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-10-16 22:09:41.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:41.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:41.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:41.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:41.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:41.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:41.377][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[2024-10-16 22:09:41.379][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:41.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:41.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:41.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:41.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:41.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:41.399][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:41.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:41.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:41.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:41.425][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:09:41.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:41.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:41.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:41.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:41.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:41.434][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:41.435][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.TRACE[2024-10-16 22:09:41.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.443][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.444][private$selectFields]
biodb.TRACE[2024-10-16 22:09:41.445][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:41.446][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:41.447][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.449][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.451][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.452][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.453][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.454][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.455][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.456][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.457][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.458][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.460][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.461][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:41.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.482][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-16 22:09:41.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:41.484][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:41.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:41.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:41.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:41.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:41.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:41.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.501][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.502][private$selectFields]
biodb.TRACE[2024-10-16 22:09:41.503][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:41.504][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:41.504][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.505][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.506][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.508][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.509][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.510][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.512][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.513][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.514][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.515][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.516][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.517][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.518][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:41.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.531][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-16 22:09:41.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:41.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:41.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:41.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:41.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:41.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:41.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:41.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.550][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.551][private$selectFields]
biodb.TRACE[2024-10-16 22:09:41.552][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:41.553][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:41.554][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.555][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.556][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.557][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.558][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.561][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.562][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.563][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:41.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.565][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.567][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.568][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:41.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:41.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.586][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-16 22:09:41.587][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:09:41.588][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:09:41.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:41.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:41.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:41.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:41.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:41.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:41.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:41.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:41.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:41.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:41.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:41.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:41.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:41.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:41.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:41.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:41.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:41.672][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[2024-10-16 22:09:41.675][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:41.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:41.679][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:41.680][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:42.090][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:42.516][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:42.520][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-10-16 22:09:42.527][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-10-16 22:09:42.533][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:42.539][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:42.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:42.545][private$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[2024-10-16 22:09:42.964][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[2024-10-16 22:09:43.385][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:43.388][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-10-16 22:09:43.392][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-10-16 22:09:43.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.404][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.407][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[2024-10-16 22:09:43.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:43.446][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.456][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:43.470][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:43.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:43.517][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:09:43.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.544][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.562][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.563][private$selectFields]
biodb.TRACE[2024-10-16 22:09:43.564][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:43.565][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:43.565][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.566][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.568][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.569][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.570][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.571][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.573][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.574][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.575][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.576][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.577][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.579][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.580][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:43.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.592][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-16 22:09:43.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.647][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.648][private$selectFields]
biodb.TRACE[2024-10-16 22:09:43.649][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:43.650][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:43.651][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.652][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.653][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.655][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.656][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.657][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.659][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.660][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.669][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.670][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.673][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.674][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:43.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.688][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-16 22:09:43.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.703][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.707][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.708][private$selectFields]
biodb.TRACE[2024-10-16 22:09:43.709][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:43.710][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:43.711][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.711][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.712][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.714][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.716][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.718][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.719][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.720][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.721][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.722][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.724][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.725][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:43.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.737][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-16 22:09:43.738][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:09:43.739][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:09:43.747][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:43.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:43.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:43.753][biodb::testThat]
biodb.INFO [2024-10-16 22:09:43.759][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-16 22:09:43.760][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:43.761][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:43.764][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:43.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:43.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:43.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:43.797][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:43.800][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:43.801][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-16 22:09:43.802][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:43.804][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-16 22:09:43.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:43.827][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:43.830][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:43.832][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-16 22:09:43.833][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:43.834][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-16 22:09:43.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.845][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.TRACE[2024-10-16 22:09:43.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.853][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:43.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.866][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.TRACE[2024-10-16 22:09:43.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.875][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:43.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:43.879][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:09:43.880][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.881][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.888][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.897][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.898][private$selectFields]
biodb.TRACE[2024-10-16 22:09:43.899][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:43.900][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:43.901][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.903][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.905][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.906][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.908][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.909][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.910][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.911][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.912][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.914][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.915][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:43.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.933][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-16 22:09:43.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.952][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.952][private$selectFields]
biodb.TRACE[2024-10-16 22:09:43.953][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:43.954][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:43.955][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.956][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.957][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.959][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.960][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.961][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.963][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.964][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.965][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:43.965][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.966][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.967][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.968][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.969][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:43.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.982][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-16 22:09:43.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:43.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:43.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:43.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:43.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:43.990][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:43.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:43.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:43.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:43.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:43.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.000][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.001][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.002][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.003][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.003][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.004][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.005][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.007][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.008][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.009][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.011][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.012][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.013][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.015][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.016][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.017][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.030][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-16 22:09:44.031][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:09:44.032][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:09:44.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.066][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[2024-10-16 22:09:44.068][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:44.071][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:44.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-16 22:09:44.074][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:44.075][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-16 22:09:44.078][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:44.081][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:44.083][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-16 22:09:44.084][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:44.085][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-16 22:09:44.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.101][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.158][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:09:44.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.168][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.179][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.180][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.181][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.182][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.183][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.184][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.185][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.186][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.187][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.189][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.190][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.191][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.192][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.193][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.195][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.196][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.208][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-16 22:09:44.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.227][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.228][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.229][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.230][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.232][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.233][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.235][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.236][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.237][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.245][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.246][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.247][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.248][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.250][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.251][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.287][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-16 22:09:44.289][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.308][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.309][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.310][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.311][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.312][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.313][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.315][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.317][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.318][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.319][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.321][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.322][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.323][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.327][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.328][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.329][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.337][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.341][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-16 22:09:44.342][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:09:44.343][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:09:44.352][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:44.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:44.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:44.359][biodb::testThat]
biodb.INFO [2024-10-16 22:09:44.360][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-16 22:09:44.361][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:44.362][biodb::testThat]
biodb.TRACE[2024-10-16 22:09:44.365][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-16 22:09:44.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-16 22:09:44.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:44.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:44.405][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:44.406][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-16 22:09:44.407][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:44.409][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-16 22:09:44.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.419][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.420][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.TRACE[2024-10-16 22:09:44.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.434][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:44.437][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:44.439][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-16 22:09:44.440][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:44.441][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-16 22:09:44.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.444][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.471][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.479][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.480][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[2024-10-16 22:09:44.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:44.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.492][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:09:44.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.502][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[2024-10-16 22:09:44.504][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.512][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.513][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.514][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.515][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.516][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.517][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.517][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.518][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.519][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.520][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.522][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.523][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.524][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.525][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.526][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.528][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.528][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.537][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.541][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-16 22:09:44.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.560][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.561][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.562][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.563][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.565][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.567][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.567][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.568][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.570][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.571][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.572][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.573][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.574][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.576][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.577][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.585][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.589][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-16 22:09:44.590][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.607][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.608][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.609][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.610][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.611][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.612][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.613][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.615][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.616][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.617][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.618][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.619][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.620][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.621][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.627][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.628][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.629][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.630][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.643][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-16 22:09:44.644][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:09:44.645][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:09:44.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:44.692][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:44.695][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:44.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-16 22:09:44.697][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:44.698][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-16 22:09:44.701][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:44.704][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:44.705][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-16 22:09:44.706][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:44.708][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-16 22:09:44.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.732][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:44.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:44.775][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-16 22:09:44.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.802][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.803][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.804][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.805][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.806][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.807][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.808][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.810][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.811][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.812][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.814][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.815][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.816][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.817][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.818][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.820][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.821][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.834][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-16 22:09:44.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.852][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.853][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.854][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.854][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.855][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.856][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.857][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.859][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.860][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.861][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.863][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.864][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.865][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.866][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.867][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.868][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.869][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.882][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-16 22:09:44.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.884][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.890][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:44.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.900][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.901][private$selectFields]
biodb.TRACE[2024-10-16 22:09:44.902][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-16 22:09:44.903][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-16 22:09:44.904][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.905][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.906][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.907][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.908][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.909][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.911][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.912][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.913][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-16 22:09:44.914][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.915][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.917][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.918][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-16 22:09:44.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:44.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:44.930][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-16 22:09:44.931][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-16 22:09:44.932][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-16 22:09:44.949][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:44.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-16 22:09:44.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:44.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:44.960][biodb::testThat]
biodb.INFO [2024-10-16 22:09:44.961][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-10-16 22:09:44.962][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:44.963][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:44.965][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-16 22:09:44.966][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:09:44.968][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-16 22:09:44.969][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:09:44.970][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:44.971][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:44.972][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:44.973][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:44.974][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:44.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:44.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:44.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:44.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:44.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:44.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:44.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:44.986][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-10-16 22:09:44.988][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:44.989][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:44.990][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-10-16 22:09:45.395][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-10-16 22:09:45.816][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:45.821][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-10-16 22:09:45.827][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-10-16 22:09:45.833][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-10-16 22:09:45.835][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:45.838][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:09:45.840][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:45.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:45.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:45.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:45.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:45.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:45.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:45.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:45.865][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.867][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.870][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.878][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:45.879][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:45.881][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.882][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.884][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:45.885][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:45.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.887][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.889][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:45.890][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:45.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.893][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.894][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:45.895][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:45.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.897][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.899][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:45.900][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:45.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.902][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.903][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:45.904][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:45.905][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.906][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.907][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:45.908][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:45.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.910][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.911][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:45.912][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:45.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.914][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.915][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:45.916][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:45.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.918][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.919][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:45.920][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:45.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.922][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:45.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:45.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:45.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:45.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:45.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:45.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:45.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:45.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:45.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:45.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:45.970][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-10-16 22:09:45.971][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-16 22:09:45.981][biodb::testThat]
biodb.INFO [2024-10-16 22:09:45.982][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-16 22:09:45.983][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:45.984][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:46.018][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-10-16 22:09:46.020][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-10-16 22:09:46.021][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-10-16 22:09:46.023][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-10-16 22:09:46.024][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-10-16 22:09:46.025][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:09:46.027][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:09:46.028][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:46.029][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:09:46.030][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:09:46.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:46.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:46.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:46.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:46.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:46.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:46.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:46.045][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-10-16 22:09:46.047][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:46.048][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:46.050][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-10-16 22:09:46.462][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-10-16 22:09:47.158][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:47.163][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-10-16 22:09:47.170][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-10-16 22:09:47.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:47.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:47.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:47.188][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:47.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:47.192][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:47.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:47.197][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-10-16 22:09:47.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:47.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:47.208][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-10-16 22:09:47.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-10-16 22:09:48.319][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:48.322][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-10-16 22:09:48.325][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-10-16 22:09:48.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:48.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:48.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:48.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:48.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:48.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:48.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:48.337][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-10-16 22:09:48.339][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:48.340][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:48.342][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-10-16 22:09:48.747][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-10-16 22:09:49.150][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:49.154][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-10-16 22:09:49.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-10-16 22:09:49.167][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-10-16 22:09:49.171][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:09:49.173][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-10-16 22:09:49.176][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-10-16 22:09:49.179][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:49.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:49.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:49.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:49.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:49.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:49.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:49.202][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.204][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.207][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.215][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:49.217][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:49.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.219][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.221][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:49.222][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:49.223][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:49.228][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:49.229][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.230][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.231][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.232][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.234][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.235][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.236][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.238][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.240][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:49.241][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:49.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.243][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.244][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.245][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.247][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.248][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:49.249][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:49.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.251][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.252][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:49.253][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:49.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.255][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.256][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:49.257][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:49.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.259][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:49.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:49.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:49.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:49.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:49.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:49.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:49.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:49.312][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.313][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.315][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.321][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:49.322][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:49.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.324][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.325][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:49.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:49.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.329][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:49.330][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:49.331][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.332][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.334][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:49.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:49.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.338][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:49.339][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:49.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.341][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.342][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:49.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:49.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.347][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.348][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.349][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.350][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.355][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.356][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.358][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.359][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.363][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:49.364][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:49.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.366][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.368][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:49.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:49.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.372][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.373][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.375][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.380][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:49.381][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:49.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.383][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:49.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:49.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.388][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:49.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:49.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.391][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.392][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:49.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:49.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.396][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:49.397][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:49.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.399][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.400][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:49.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:49.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:49.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:49.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:49.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:49.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:49.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:49.441][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:49.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:09:49.445][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.446][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.448][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.458][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:49.460][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:49.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.461][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.463][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:09:49.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:09:49.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.467][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:49.468][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:49.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.470][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:09:49.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:09:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.481][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:49.482][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:49.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.484][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:09:49.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:09:49.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.490][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.491][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.493][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:09:49.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.499][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.500][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.502][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.503][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:09:49.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.508][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:49.509][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:49.510][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.511][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.512][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:09:49.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:09:49.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.517][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.518][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.520][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:49.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.526][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:49.527][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:49.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.529][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:49.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:49.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.535][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:49.536][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:49.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.538][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:09:49.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:09:49.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.543][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:49.544][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:49.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.546][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.548][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:09:49.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:09:49.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:09:49.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:49.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:09:49.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:09:49.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:49.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:09:49.620][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-10-16 22:09:49.621][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-16 22:09:49.622][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-16 22:09:49.649][biodb::testThat]
biodb.INFO [2024-10-16 22:09:49.651][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-10-16 22:09:49.652][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:49.653][biodb::testThat]
biodb.INFO [2024-10-16 22:09:49.676][biodb::testThat]
biodb.INFO [2024-10-16 22:09:49.677][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-10-16 22:09:49.678][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:49.679][biodb::testThat]
biodb.INFO [2024-10-16 22:09:49.686][biodb::testThat]
biodb.INFO [2024-10-16 22:09:49.687][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-10-16 22:09:49.688][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:49.689][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:49.692][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:49.695][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:49.696][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:49.698][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:50.164][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:50.931][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:50.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-10-16 22:09:50.937][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-10-16 22:09:50.948][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:09:50.949][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:09:50.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:50.951][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:09:50.952][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:50.953][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:09:50.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:09:50.955][ef$get] fields variable is a list.
biodb.INFO [2024-10-16 22:09:50.956][biodb::testThat]
biodb.INFO [2024-10-16 22:09:50.957][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-16 22:09:50.958][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:50.959][biodb::testThat]
biodb.ERROR[2024-10-16 22:09:50.972][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-16 22:09:50.989][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-16 22:09:51.002][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:09:51.003][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-16 22:09:51.004][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-16 22:09:51.005][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:09:51.006][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.007][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.009][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:09:51.019][biodb::testContext]
biodb.INFO [2024-10-16 22:09:51.020][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:51.021][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-10-16 22:09:51.022][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:51.023][biodb::testContext]
biodb.INFO [2024-10-16 22:09:51.025][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:51.027][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:51.030][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:51.031][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:09:51.032][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:09:51.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.035][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[2024-10-16 22:09:51.036][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:09:51.037][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:09:51.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.049][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:09:51.051][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:09:51.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.053][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[2024-10-16 22:09:51.054][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:09:51.055][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:09:51.056][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:09:51.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.060][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:09:51.061][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:09:51.062][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:09:51.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.064][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.DEBUG[2024-10-16 22:09:51.065][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:09:51.066][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:09:51.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.069][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:09:51.070][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:09:51.071][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:09:51.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.075][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:09:51.076][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:09:51.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.079][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:09:51.080][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:09:51.081][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:09:51.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.083][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.DEBUG[2024-10-16 22:09:51.084][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:51.085][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:09:51.086][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:09:51.087][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:09:51.088][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:09:51.089][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:09:51.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.092][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:09:51.093][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:09:51.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.096][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[2024-10-16 22:09:51.097][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:09:51.098][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:09:51.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.101][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:09:51.102][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:09:51.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.105][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[2024-10-16 22:09:51.105][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:09:51.106][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:09:51.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.110][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:09:51.111][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:09:51.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.113][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[2024-10-16 22:09:51.114][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:51.115][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:09:51.118][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:09:51.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.121][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:09:51.122][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:09:51.123][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:09:51.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.126][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[2024-10-16 22:09:51.127][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:09:51.129][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.130][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:09:51.131][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.132][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:51.133][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.134][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.134][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.135][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.136][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:51.137][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:51.138][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.139][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:09:51.140][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:51.141][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.142][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.143][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:51.143][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:51.143][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:51.143][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:51.143][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:51.144][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:51.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.146][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.146][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:51.147][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.148][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.149][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.150][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.151][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:51.152][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:51.153][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.154][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.155][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:09:51.156][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.157][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:51.158][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.159][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:51.160][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.161][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.162][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.163][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.164][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:51.165][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:51.166][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.167][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:09:51.167][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:51.168][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.169][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.170][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:51.170][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:51.170][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:51.170][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:51.170][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:51.171][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:51.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.173][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.174][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:51.175][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.176][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.176][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.177][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.178][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:51.179][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:51.180][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.181][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.182][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:09:51.184][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.185][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:09:51.186][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.186][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:51.187][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.188][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.189][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.190][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.191][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:51.192][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:51.193][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.194][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:09:51.195][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:51.196][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.197][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.198][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.199][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:51.199][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.392][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:51.393][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.395][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.396][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.397][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:51.397][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:51.398][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.399][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.400][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:09:51.402][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.403][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:51.404][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.405][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:51.405][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.406][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.407][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.408][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.409][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:51.410][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:51.411][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.412][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:09:51.413][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:51.414][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.414][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.415][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.416][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:51.417][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.419][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:51.420][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.421][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.422][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.423][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:51.424][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:51.425][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.426][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:51.427][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:51.428][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.428][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[2024-10-16 22:09:51.429][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.432][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[2024-10-16 22:09:51.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.436][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[2024-10-16 22:09:51.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.453][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.480][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[2024-10-16 22:09:51.481][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.484][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[2024-10-16 22:09:51.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.497][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:09:51.499][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:09:51.500][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:09:51.501][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:09:51.503][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:51.504][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:51.505][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:51.506][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:51.508][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:09:51.509][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:51.510][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:51.512][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:09:51.513][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:51.514][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:51.515][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:09:51.517][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:51.518][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:09:51.519][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:09:51.521][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:51.522][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:09:51.523][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:09:51.525][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:09:51.526][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:09:51.527][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:09:51.528][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:09:51.530][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:09:51.531][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:09:51.532][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:09:51.534][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:09:51.535][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:09:51.536][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:09:51.538][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:09:51.539][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:09:51.540][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:09:51.545][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:09:51.547][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:09:51.548][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:09:51.549][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:09:51.550][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:09:51.552][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:09:51.553][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:09:51.554][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:09:51.555][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:09:51.556][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:09:51.558][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:09:51.559][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:09:51.560][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:09:51.561][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:09:51.563][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:09:51.564][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:09:51.565][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:09:51.566][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:09:51.568][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:09:51.569][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:09:51.570][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:09:51.571][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:09:51.573][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:09:51.574][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:09:51.575][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:09:51.576][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:09:51.577][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:09:51.583][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:09:51.585][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:09:51.586][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:09:51.588][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:09:51.589][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:09:51.591][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:51.592][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:51.593][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:09:51.595][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:09:51.596][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:09:51.598][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:09:51.599][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:09:51.600][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:09:51.602][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:09:51.603][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:09:51.604][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:09:51.606][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:09:51.607][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:09:51.609][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:09:51.610][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:09:51.611][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:09:51.613][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:09:51.614][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:09:51.616][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:51.618][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:51.618][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.620][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.622][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.627][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[2024-10-16 22:09:51.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.640][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[2024-10-16 22:09:51.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.646][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[2024-10-16 22:09:51.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.653][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.672][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[2024-10-16 22:09:51.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.711][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.730][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:51.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:51.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:51.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:51.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:51.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:51.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:51.742][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:51.744][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-16 22:09:51.746][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.747][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.748][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.749][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:51.749][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.750][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.751][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.752][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-16 22:09:51.753][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-16 22:09:51.754][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:51.755][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.756][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-16 22:09:51.757][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-16 22:09:51.758][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-16 22:09:51.759][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:51.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:51.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:51.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:51.761][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-16 22:09:51.762][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.763][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.764][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:51.765][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:51.766][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:51.766][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:51.767][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:51.767][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-16 22:09:51.768][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:51.769][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:51.770][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:51.771][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-16 22:09:51.771][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-16 22:09:51.772][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:51.773][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:51.775][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-16 22:09:51.776][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:51.777][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:51.779][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:51.782][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-16 22:09:51.783][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-16 22:09:51.784][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-16 22:09:51.785][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-16 22:09:51.786][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:51.787][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:51.788][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-16 22:09:51.789][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-16 22:09:51.791][biodb::testThat]
biodb.INFO [2024-10-16 22:09:51.791][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-10-16 22:09:51.792][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:51.793][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:51.797][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-16 22:09:51.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:51.801][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:51.802][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-10-16 22:09:52.427][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-10-16 22:09:52.982][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:52.987][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-10-16 22:09:53.021][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-10-16 22:09:53.028][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:53.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:53.035][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:53.037][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:53.449][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:53.859][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:53.864][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-10-16 22:09:53.870][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-10-16 22:09:53.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:53.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:53.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:53.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:53.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:53.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:53.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:53.883][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:53.887][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:53.888][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:53.889][private$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[2024-10-16 22:09:54.297][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[2024-10-16 22:09:54.701][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:54.705][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-10-16 22:09:54.712][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-10-16 22:09:54.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:54.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:54.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:54.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:54.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:54.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:54.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:54.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:54.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:54.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:54.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:54.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:54.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:54.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:54.789][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:54.792][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:54.793][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-16 22:09:54.794][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:54.795][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-16 22:09:54.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:54.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:54.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:54.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:54.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:54.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:54.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:54.807][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:54.809][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:54.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-16 22:09:54.812][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:54.813][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-16 22:09:54.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:54.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:54.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:54.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:54.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:54.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:54.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:54.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:54.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:54.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:54.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:54.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:54.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:54.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:54.835][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:54.838][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:54.839][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-16 22:09:54.840][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:54.842][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-16 22:09:54.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:54.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:54.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:54.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:54.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:54.850][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:54.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:54.853][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:54.856][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:54.857][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-16 22:09:54.858][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:54.859][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-16 22:09:54.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:54.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:54.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:54.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:54.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:54.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:54.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:54.871][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:54.873][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:54.874][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:54.876][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:55.278][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:55.699][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:55.703][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-10-16 22:09:55.708][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-10-16 22:09:55.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:55.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:55.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:55.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:55.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:55.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:55.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:09:55.730][biodb::testThat]
biodb.INFO [2024-10-16 22:09:55.732][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-10-16 22:09:55.733][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:55.734][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:55.738][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:55.742][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:55.743][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:55.745][private$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[2024-10-16 22:09:56.156][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[2024-10-16 22:09:56.564][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:56.569][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-10-16 22:09:56.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-10-16 22:09:56.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:56.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:56.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:56.628][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:56.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:56.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:56.632][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[2024-10-16 22:09:56.637][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:56.641][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:56.643][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:56.645][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-16 22:09:57.067][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-16 22:09:57.711][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:57.713][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-10-16 22:09:57.717][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-10-16 22:09:57.720][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:09:57.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:57.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:57.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:09:57.734][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:09:57.735][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-16 22:09:57.736][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-16 22:09:57.737][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:09:57.738][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:57.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:57.740][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.742][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:09:57.746][biodb::testContext]
biodb.INFO [2024-10-16 22:09:57.747][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:57.748][biodb::testContext] Test context - Test web services
biodb.INFO [2024-10-16 22:09:57.749][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:57.750][biodb::testContext]
biodb.INFO [2024-10-16 22:09:57.752][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:57.754][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:57.758][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:57.759][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:09:57.760][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:09:57.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.763][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:09:57.765][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:09:57.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.768][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:09:57.769][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:09:57.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.773][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:09:57.774][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:09:57.775][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:09:57.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.779][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:09:57.780][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:09:57.781][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:09:57.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.783][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.DEBUG[2024-10-16 22:09:57.784][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:09:57.785][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:09:57.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.789][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:09:57.790][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:09:57.791][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:09:57.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.795][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:09:57.796][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:09:57.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.799][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:09:57.800][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:09:57.801][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:09:57.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.805][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:57.806][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:09:57.807][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:09:57.808][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:09:57.809][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:09:57.810][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:09:57.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.814][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:09:57.815][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:09:57.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.818][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:09:57.819][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:09:57.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.823][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:09:57.824][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:09:57.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.827][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:09:57.828][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:09:57.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.832][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:09:57.833][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:09:57.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.836][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:57.837][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:09:57.840][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:09:57.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.844][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:09:57.845][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:09:57.846][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:09:57.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.849][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:09:57.851][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.852][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:09:57.853][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.854][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:57.855][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.856][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.857][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.858][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.859][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:57.860][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:57.861][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.862][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:09:57.863][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:57.872][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.873][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.874][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:57.874][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:57.874][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:57.874][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:57.874][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:57.875][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:57.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:57.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:57.877][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:57.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:57.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:57.880][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.881][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.882][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:57.882][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:57.883][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.884][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.885][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:09:57.887][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.888][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:57.889][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.890][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:57.891][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.893][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.894][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:57.895][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:57.896][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.897][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:09:57.898][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:57.899][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.900][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.901][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:57.901][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:57.901][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:57.901][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:57.901][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:57.902][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:57.903][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:57.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:57.905][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:57.905][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:57.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:57.907][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.908][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.909][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:57.910][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:57.911][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.912][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.913][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:09:57.914][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.915][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:09:57.916][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.917][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:57.918][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.919][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.920][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.921][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.922][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:57.923][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:57.924][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.924][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:09:57.925][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:57.926][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.927][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.928][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.929][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:57.930][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:57.931][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:57.932][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:57.933][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:57.934][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:57.935][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.936][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.937][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:57.938][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:57.939][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.939][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.940][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:09:57.942][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.943][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:57.944][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.945][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:57.946][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.947][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.948][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.949][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.950][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:57.950][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:57.951][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.952][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:09:57.953][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:57.954][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.955][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:57.956][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.957][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:57.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:57.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:57.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:57.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:57.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:57.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:57.963][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.964][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:57.965][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:57.966][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:57.967][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:57.968][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:57.969][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.978][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.DEBUG[2024-10-16 22:09:57.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:57.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.995][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[2024-10-16 22:09:57.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:57.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:57.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:57.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:57.999][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[2024-10-16 22:09:58.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.004][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[2024-10-16 22:09:58.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.008][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[2024-10-16 22:09:58.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.017][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[2024-10-16 22:09:58.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.035][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[2024-10-16 22:09:58.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.039][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[2024-10-16 22:09:58.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.044][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[2024-10-16 22:09:58.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.049][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:09:58.051][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:09:58.052][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:09:58.054][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:09:58.055][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:58.056][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:58.058][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:58.059][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:58.060][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:09:58.062][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:58.063][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:58.065][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:09:58.066][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:58.067][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:58.069][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:09:58.070][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:58.071][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:09:58.073][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:09:58.074][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:58.075][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:09:58.077][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:09:58.078][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:09:58.079][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:09:58.081][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:09:58.082][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:09:58.084][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:09:58.085][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:09:58.086][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:09:58.088][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:09:58.089][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:09:58.090][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:09:58.092][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:09:58.093][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:09:58.094][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:09:58.096][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:09:58.097][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:09:58.098][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:09:58.100][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:09:58.101][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:09:58.102][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:09:58.104][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:09:58.105][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:09:58.106][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:09:58.108][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:09:58.109][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:09:58.111][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:09:58.112][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:09:58.113][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:09:58.114][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:09:58.116][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:09:58.117][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:09:58.118][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:09:58.120][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:09:58.121][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:09:58.122][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:09:58.123][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:09:58.125][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:09:58.126][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:09:58.127][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:09:58.128][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:09:58.130][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:09:58.131][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:09:58.132][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:09:58.134][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:09:58.135][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:09:58.136][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:09:58.137][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:58.139][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:58.140][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:09:58.141][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:09:58.143][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:09:58.144][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:09:58.145][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:09:58.147][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:09:58.148][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:09:58.149][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:09:58.151][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:09:58.152][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:09:58.153][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:09:58.155][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:09:58.156][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:09:58.157][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:09:58.159][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:09:58.160][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:09:58.162][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:58.163][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:58.163][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.165][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.166][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[2024-10-16 22:09:58.167][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.172][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[2024-10-16 22:09:58.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.223][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[2024-10-16 22:09:58.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.252][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[2024-10-16 22:09:58.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:58.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:58.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:58.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:58.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:58.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:58.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:58.270][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[2024-10-16 22:09:58.272][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:58.273][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-16 22:09:58.278][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:58.280][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:09:58.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:58.282][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:58.283][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:58.284][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:58.285][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:58.286][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-16 22:09:58.287][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-16 22:09:58.288][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:58.289][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:58.291][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-16 22:09:58.292][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-16 22:09:58.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-16 22:09:58.294][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:58.295][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:58.295][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:58.295][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:58.296][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-16 22:09:58.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:58.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:58.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:58.301][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:58.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:58.303][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:58.304][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:09:58.304][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-16 22:09:58.305][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:58.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:58.307][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:58.308][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-16 22:09:58.308][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-16 22:09:58.310][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:58.312][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:58.314][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-16 22:09:58.315][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:58.317][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:58.319][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:58.323][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-16 22:09:58.325][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-16 22:09:58.326][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-16 22:09:58.328][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-16 22:09:58.329][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:58.330][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:09:58.332][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-16 22:09:58.333][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-16 22:09:58.334][biodb::testThat]
biodb.INFO [2024-10-16 22:09:58.335][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-10-16 22:09:58.336][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:09:58.337][biodb::testThat]
biodb.DEBUG[2024-10-16 22:09:58.341][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-16 22:09:58.345][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:09:58.347][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-16 22:09:58.348][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:09:58.350][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-16 22:09:58.354][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:09:58.357][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:09:58.358][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:09:58.360][private$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[2024-10-16 22:09:59.025][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[2024-10-16 22:09:59.451][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:09:59.453][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-10-16 22:09:59.457][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-10-16 22:09:59.465][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:09:59.466][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-16 22:09:59.467][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-16 22:09:59.468][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:09:59.469][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.470][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.472][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-16 22:09:59.477][biodb::testContext]
biodb.INFO [2024-10-16 22:09:59.478][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:59.478][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-10-16 22:09:59.479][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-16 22:09:59.480][biodb::testContext]
biodb.INFO [2024-10-16 22:09:59.482][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:59.484][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:59.488][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:59.489][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-16 22:09:59.490][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-16 22:09:59.491][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.493][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-16 22:09:59.494][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-16 22:09:59.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.498][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-16 22:09:59.499][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-16 22:09:59.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.502][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-16 22:09:59.503][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-16 22:09:59.504][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-16 22:09:59.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.508][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-16 22:09:59.509][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-16 22:09:59.510][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-16 22:09:59.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.513][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-16 22:09:59.514][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-16 22:09:59.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.518][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-16 22:09:59.519][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-16 22:09:59.520][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-16 22:09:59.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.523][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-16 22:09:59.525][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-16 22:09:59.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.528][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-16 22:09:59.529][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-16 22:09:59.530][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-16 22:09:59.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.534][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:59.535][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-16 22:09:59.536][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-16 22:09:59.537][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-16 22:09:59.537][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-16 22:09:59.539][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-16 22:09:59.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.542][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-16 22:09:59.543][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-16 22:09:59.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.546][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-16 22:09:59.547][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-16 22:09:59.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.551][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-16 22:09:59.551][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-16 22:09:59.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.555][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-16 22:09:59.556][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-16 22:09:59.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.559][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-16 22:09:59.560][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-16 22:09:59.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.563][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-16 22:09:59.564][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-16 22:09:59.567][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-16 22:09:59.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.570][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-16 22:09:59.571][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-16 22:09:59.572][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-16 22:09:59.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.575][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-16 22:09:59.577][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.578][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-16 22:09:59.579][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.580][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:59.581][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.582][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.583][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.584][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.584][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:59.585][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:59.586][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.587][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-16 22:09:59.588][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:59.589][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.590][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.591][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:59.591][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:59.591][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:59.591][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:59.591][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:59.592][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:59.593][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.595][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:59.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.597][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.598][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.599][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:59.600][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:59.601][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.601][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.603][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-16 22:09:59.604][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.605][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:59.606][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.607][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:59.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.615][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.616][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.617][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:59.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:59.619][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.620][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-16 22:09:59.621][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:59.622][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.623][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.624][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:59.624][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:59.624][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:59.624][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-16 22:09:59.624][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-16 22:09:59.625][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:59.625][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.627][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:59.628][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.630][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.631][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.632][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:59.632][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:59.633][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.634][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.635][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-16 22:09:59.637][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.638][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-16 22:09:59.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:59.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.645][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-16 22:09:59.646][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:59.647][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.648][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-16 22:09:59.649][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:59.649][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.650][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.651][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.652][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:59.653][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.654][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.655][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:59.656][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.658][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.659][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.660][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:59.660][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:59.661][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.662][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.663][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-16 22:09:59.665][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.666][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-16 22:09:59.667][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.667][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:59.668][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.669][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.670][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.671][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.672][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-16 22:09:59.673][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:59.674][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.675][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-16 22:09:59.675][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:59.676][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.677][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.678][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.679][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-16 22:09:59.680][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.681][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.682][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:59.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.684][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.685][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.686][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:09:59.687][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:09:59.687][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.688][self$setPropertyValue]
biodb.DEBUG[2024-10-16 22:09:59.690][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:59.690][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.695][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[2024-10-16 22:09:59.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.699][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[2024-10-16 22:09:59.700][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.703][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[2024-10-16 22:09:59.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.719][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[2024-10-16 22:09:59.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.748][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[2024-10-16 22:09:59.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.756][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.DEBUG[2024-10-16 22:09:59.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.765][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-16 22:09:59.766][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-16 22:09:59.768][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-16 22:09:59.769][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-16 22:09:59.770][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:09:59.771][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-16 22:09:59.772][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:59.774][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:59.775][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-16 22:09:59.776][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-16 22:09:59.777][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:09:59.779][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-16 22:09:59.780][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-16 22:09:59.781][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-16 22:09:59.782][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-16 22:09:59.784][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-16 22:09:59.785][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-16 22:09:59.786][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-16 22:09:59.787][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:09:59.789][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-16 22:09:59.790][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-16 22:09:59.791][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-16 22:09:59.792][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-16 22:09:59.794][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-16 22:09:59.795][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-16 22:09:59.796][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-16 22:09:59.797][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-16 22:09:59.798][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-16 22:09:59.800][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-16 22:09:59.801][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-16 22:09:59.802][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-16 22:09:59.803][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-16 22:09:59.805][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-16 22:09:59.806][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-16 22:09:59.807][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-16 22:09:59.808][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-16 22:09:59.810][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-16 22:09:59.811][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-16 22:09:59.812][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-16 22:09:59.813][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-16 22:09:59.815][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-16 22:09:59.816][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-16 22:09:59.817][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-16 22:09:59.818][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-16 22:09:59.819][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-16 22:09:59.821][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-16 22:09:59.822][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-16 22:09:59.823][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-16 22:09:59.824][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-16 22:09:59.826][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-16 22:09:59.827][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-16 22:09:59.828][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-16 22:09:59.829][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-16 22:09:59.831][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-16 22:09:59.832][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-16 22:09:59.833][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-16 22:09:59.834][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-16 22:09:59.836][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-16 22:09:59.837][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-16 22:09:59.838][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-16 22:09:59.839][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-16 22:09:59.840][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-16 22:09:59.842][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-16 22:09:59.843][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-16 22:09:59.844][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-16 22:09:59.845][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-16 22:09:59.847][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:09:59.848][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:09:59.849][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-16 22:09:59.850][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-16 22:09:59.851][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-16 22:09:59.853][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-16 22:09:59.854][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-16 22:09:59.855][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-16 22:09:59.856][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-16 22:09:59.858][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-16 22:09:59.859][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-16 22:09:59.860][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-16 22:09:59.861][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-16 22:09:59.863][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-16 22:09:59.864][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-16 22:09:59.865][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-16 22:09:59.866][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-16 22:09:59.868][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-16 22:09:59.869][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-16 22:09:59.870][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-16 22:09:59.871][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.873][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.897][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[2024-10-16 22:09:59.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.902][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[2024-10-16 22:09:59.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.935][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[2024-10-16 22:09:59.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.952][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[2024-10-16 22:09:59.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.960][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.969][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[2024-10-16 22:09:59.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-16 22:09:59.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:09:59.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:09:59.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:09:59.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:09:59.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:09:59.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-16 22:09:59.976][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-16 22:09:59.977][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-16 22:09:59.979][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.980][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.981][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.982][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-16 22:09:59.983][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.984][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-16 22:09:59.984][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.985][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-16 22:09:59.986][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-16 22:09:59.987][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-16 22:09:59.988][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-16 22:09:59.989][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-16 22:09:59.990][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-16 22:09:59.991][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-16 22:09:59.992][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-16 22:09:59.993][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-16 22:09:59.993][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-16 22:09:59.993][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-16 22:09:59.994][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-16 22:09:59.995][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.995][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.996][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-16 22:09:59.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-16 22:09:59.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-16 22:09:59.999][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-16 22:10:00.000][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:10:00.000][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-16 22:10:00.001][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-16 22:10:00.001][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-16 22:10:00.002][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-16 22:10:00.003][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-16 22:10:00.003][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-16 22:10:00.004][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-16 22:10:00.006][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-16 22:10:00.007][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-16 22:10:00.008][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-16 22:10:00.010][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-16 22:10:00.011][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-16 22:10:00.014][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-16 22:10:00.015][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-16 22:10:00.016][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-16 22:10:00.017][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-16 22:10:00.018][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:10:00.019][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-16 22:10:00.021][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-16 22:10:00.021][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-16 22:10:00.023][biodb::testThat]
biodb.INFO [2024-10-16 22:10:00.024][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-10-16 22:10:00.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-16 22:10:00.025][biodb::testThat]
biodb.DEBUG[2024-10-16 22:10:00.028][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-16 22:10:00.031][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:10:00.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-16 22:10:00.034][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:10:00.035][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-16 22:10:00.038][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-16 22:10:00.041][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-16 22:10:00.042][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-10-16 22:10:00.043][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-16 22:10:00.044][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-10-16 22:10:00.048][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-10-16 22:10:00.049][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-16 22:10:00.050][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-10-16 22:10:00.051][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-16 22:10:00.052][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-16 22:10:00.053][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-16 22:10:00.054][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-16 22:10:00.055][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-16 22:10:00.056][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-16 22:10:00.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:00.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:00.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:00.068][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:00.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:00.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:00.071][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[2024-10-16 22:10:00.072][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-10-16 22:10:00.074][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-16 22:10:00.075][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-16 22:10:00.076][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-10-16 22:10:00.496][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-10-16 22:10:01.702][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-16 22:10:01.710][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-10-16 22:10:01.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-10-16 22:10:01.725][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-10-16 22:10:01.729][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-16 22:10:01.732][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-16 22:10:01.734][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-16 22:10:01.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-16 22:10:01.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:01.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:01.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:01.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:01.752][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:01.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-16 22:10:01.761][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.762][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.764][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.771][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:10:01.772][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:10:01.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.774][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.776][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-16 22:10:01.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-16 22:10:01.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.780][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:10:01.781][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:10:01.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.783][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.784][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-16 22:10:01.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-16 22:10:01.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.788][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-16 22:10:01.790][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-16 22:10:01.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.791][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.793][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-16 22:10:01.794][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-16 22:10:01.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.796][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.797][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:10:01.799][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:10:01.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.801][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.802][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:10:01.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-16 22:10:01.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.806][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:10:01.807][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:10:01.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.809][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.810][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-16 22:10:01.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-16 22:10:01.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.814][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:01.816][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:01.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.818][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:01.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-16 22:10:01.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.823][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:01.824][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:01.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.826][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.828][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-16 22:10:01.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-16 22:10:01.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.832][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:10:01.833][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:10:01.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.835][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.836][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-16 22:10:01.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-16 22:10:01.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.840][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:10:01.841][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:10:01.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.843][ef$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.845][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-16 22:10:01.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-16 22:10:01.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:10:01.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:10:01.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:10:01.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:10:01.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-16 22:10:01.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-16 22:10:01.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-16 22:10:01.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-16 22:10:01.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-16 22:10:01.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-16 22:10:01.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-16 22:10:01.936][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-10-16 22:10:01.939][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-16 22:10:01.940][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-16 22:10:01.941][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-16 22:10:01.942][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-16 22:10:01.943][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-16 22:10:01.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-16 22:10:01.944][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-16 22:10:01.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-16 22:10:01.946][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-16 22:10:01.947][FUN] Functions in observer 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 386 ]
> 
> proc.time()
   user  system elapsed 
 23.828   1.396  65.525

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	0.970	0.059	1.940
ChebiEntry	0.150	0.012	0.163