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This page was generated on 2023-05-26 06:18:04 -0000 (Fri, 26 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4254
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CHECK results for biodbChebi on kunpeng2


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 191/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.7.0  (landing page)
Pierrick Roger
Snapshot Date: 2023-05-25 13:29:39 -0000 (Thu, 25 May 2023)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: 8404aa9
git_last_commit_date: 2023-04-25 15:32:59 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: biodbChebi
Version: 1.7.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biodbChebi_1.7.0.tar.gz
StartedAt: 2023-05-26 04:06:41 -0000 (Fri, 26 May 2023)
EndedAt: 2023-05-26 04:11:45 -0000 (Fri, 26 May 2023)
EllapsedTime: 304.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings biodbChebi_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/biodbChebi.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.7.0’
* 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 R 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘biodbChebi.Rmd’ using ‘UTF-8’... OK
 NONE
* 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/R/R-4.3.0/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

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 [2023-05-26 04:08:12.353][biodb::testContext]
biodb.INFO [2023-05-26 04:08:12.356][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:08:12.358][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-05-26 04:08:12.359][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:08:12.360][biodb::testContext]
biodb.INFO [2023-05-26 04:08:12.381][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:08:12.384][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-26 04:08:12.393][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:08:12.395][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-26 04:08:12.397][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-26 04:08:12.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.402][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-26 04:08:12.430][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-26 04:08:12.432][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.436][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-26 04:08:12.438][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-26 04:08:12.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.443][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-26 04:08:12.445][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-26 04:08:12.447][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-26 04:08:12.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.451][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[2023-05-26 04:08:12.453][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-26 04:08:12.454][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-26 04:08:12.456][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-26 04:08:12.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.462][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-26 04:08:12.464][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-26 04:08:12.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.468][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[2023-05-26 04:08:12.469][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-26 04:08:12.471][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-26 04:08:12.472][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-26 04:08:12.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.478][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-26 04:08:12.479][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-26 04:08:12.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.484][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-26 04:08:12.486][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-26 04:08:12.487][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-26 04:08:12.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.493][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:08:12.494][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-26 04:08:12.495][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-26 04:08:12.497][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-26 04:08:12.498][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-26 04:08:12.500][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-26 04:08:12.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.505][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-26 04:08:12.507][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-26 04:08:12.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.512][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-26 04:08:12.513][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-26 04:08:12.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.517][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[2023-05-26 04:08:12.518][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-26 04:08:12.520][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-26 04:08:12.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.525][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-26 04:08:12.527][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-26 04:08:12.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.531][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.DEBUG[2023-05-26 04:08:12.532][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-26 04:08:12.534][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-26 04:08:12.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.539][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:08:12.540][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-26 04:08:12.546][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-26 04:08:12.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.550][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[2023-05-26 04:08:12.551][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-26 04:08:12.553][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-26 04:08:12.554][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-26 04:08:12.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.564][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-26 04:08:12.615][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.653][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-26 04:08:12.654][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.656][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:12.657][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.658][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.660][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.661][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.662][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:08:12.664][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:12.665][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.667][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-26 04:08:12.668][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:12.669][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.671][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.672][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:08:12.672][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:08:12.672][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:08:12.672][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:08:12.672][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:08:12.673][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:12.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:12.676][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:12.677][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:12.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:12.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:12.681][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.683][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:12.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:12.687][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.688][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.689][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-26 04:08:12.692][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.694][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:08:12.695][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.696][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:12.698][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.699][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.700][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.701][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.703][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:08:12.704][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:12.706][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.707][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-26 04:08:12.708][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:12.710][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.711][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.712][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:08:12.712][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:08:12.712][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:08:12.712][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:08:12.712][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:08:12.714][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:12.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:12.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:12.718][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:12.719][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:12.720][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:12.721][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.723][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.724][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:12.725][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:12.726][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.728][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.729][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-26 04:08:12.732][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.733][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-26 04:08:12.734][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.736][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:12.737][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.738][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.740][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.741][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.742][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:08:12.744][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:12.745][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.746][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-26 04:08:12.748][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:12.749][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.750][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.752][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.753][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:12.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:12.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:12.757][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:12.758][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:12.759][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:12.760][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.762][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.763][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:12.764][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:12.765][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.767][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.768][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-26 04:08:12.770][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.772][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:08:12.773][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.774][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:12.776][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.779][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.780][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.782][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.783][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:08:12.784][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:12.786][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.787][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-26 04:08:12.788][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:12.790][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.791][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:12.792][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.793][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:08:12.795][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:12.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:12.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:12.798][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:12.800][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:12.801][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:12.802][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.803][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:12.805][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:12.806][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:12.807][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:08:12.812][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:08:12.813][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.826][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[2023-05-26 04:08:12.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.832][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[2023-05-26 04:08:12.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.879][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[2023-05-26 04:08:12.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.885][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[2023-05-26 04:08:12.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.891][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[2023-05-26 04:08:12.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.897][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[2023-05-26 04:08:12.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:12.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:12.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:12.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:12.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:12.916][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-26 04:08:12.922][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-26 04:08:12.925][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-26 04:08:12.927][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-26 04:08:12.929][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:08:12.931][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-26 04:08:12.933][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-26 04:08:12.935][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-26 04:08:12.937][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-26 04:08:12.939][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-26 04:08:12.942][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:08:12.944][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-26 04:08:12.946][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-26 04:08:12.948][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-26 04:08:12.949][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-26 04:08:12.951][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:08:12.953][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-26 04:08:12.955][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-26 04:08:12.957][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:08:12.959][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-26 04:08:12.961][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-26 04:08:12.963][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-26 04:08:12.965][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-26 04:08:12.967][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-26 04:08:12.968][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-26 04:08:12.970][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-26 04:08:12.972][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-26 04:08:12.974][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-26 04:08:12.976][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-26 04:08:12.978][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-26 04:08:12.980][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-26 04:08:12.990][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-26 04:08:12.992][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-26 04:08:12.994][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-26 04:08:12.996][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-26 04:08:12.998][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-26 04:08:13.000][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-26 04:08:13.002][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-26 04:08:13.004][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-26 04:08:13.006][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-26 04:08:13.008][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-26 04:08:13.010][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-26 04:08:13.012][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-26 04:08:13.014][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-26 04:08:13.016][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-26 04:08:13.018][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-26 04:08:13.020][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-26 04:08:13.022][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-26 04:08:13.024][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-26 04:08:13.026][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-26 04:08:13.028][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-26 04:08:13.030][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-26 04:08:13.032][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-26 04:08:13.034][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-26 04:08:13.036][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-26 04:08:13.038][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-26 04:08:13.040][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-26 04:08:13.042][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-26 04:08:13.044][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-26 04:08:13.046][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-26 04:08:13.048][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-26 04:08:13.050][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-26 04:08:13.052][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-26 04:08:13.054][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-26 04:08:13.056][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-26 04:08:13.058][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-26 04:08:13.060][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:08:13.062][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:08:13.064][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-26 04:08:13.066][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-26 04:08:13.068][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-26 04:08:13.069][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-26 04:08:13.071][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-26 04:08:13.073][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-26 04:08:13.075][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-26 04:08:13.077][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-26 04:08:13.080][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-26 04:08:13.082][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-26 04:08:13.084][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-26 04:08:13.086][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-26 04:08:13.088][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-26 04:08:13.090][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-26 04:08:13.092][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-26 04:08:13.100][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-26 04:08:13.103][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:08:13.107][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:08:13.108][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.111][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.126][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[2023-05-26 04:08:13.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.144][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.168][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.DEBUG[2023-05-26 04:08:13.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.177][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[2023-05-26 04:08:13.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:08:13.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:13.271][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-05-26 04:08:13.285][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-05-26 04:08:13.288][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:13.289][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-26 04:08:13.291][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:13.293][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:08:13.294][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:13.296][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:08:13.297][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:13.299][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-05-26 04:08:13.300][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-26 04:08:13.302][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:08:13.303][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:13.305][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-05-26 04:08:13.306][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-05-26 04:08:13.307][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-05-26 04:08:13.309][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-26 04:08:13.310][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:08:13.310][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:08:13.310][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:08:13.311][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-26 04:08:13.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:13.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:13.315][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:08:13.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:08:13.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:08:13.319][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:08:13.320][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:08:13.320][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-05-26 04:08:13.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:08:13.323][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:08:13.324][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-26 04:08:13.326][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-05-26 04:08:13.326][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-05-26 04:08:13.334][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:08:13.345][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:08:13.347][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-05-26 04:08:13.349][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:08:13.352][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:08:13.354][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:08:13.386][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-05-26 04:08:13.388][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-05-26 04:08:13.394][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-05-26 04:08:13.400][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-05-26 04:08:13.406][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-26 04:08:13.407][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-26 04:08:13.409][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-05-26 04:08:13.410][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-05-26 04:08:13.433][biodb::testThat]
biodb.INFO [2023-05-26 04:08:13.434][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2023-05-26 04:08:13.435][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:13.437][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:13.442][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/R/R-4.3.0/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2023-05-26 04:08:13.449][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:13.453][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:08:13.464][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:13.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:13.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:13.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:13.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:13.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:13.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:13.501][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.502][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.503][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.505][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.532][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:13.534][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:13.535][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.536][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.574][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:13.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:13.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.583][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:13.585][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:13.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.587][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.589][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:13.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:13.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.598][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:13.599][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:13.601][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.602][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:13.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:13.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.613][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:13.614][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:13.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.617][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:13.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:13.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.628][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:13.630][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:13.631][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.632][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.634][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:13.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:13.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.643][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:13.645][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:13.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.648][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.649][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:13.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:13.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.659][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:13.660][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:13.662][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.663][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:13.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:13.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.674][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:13.676][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:13.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.679][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:13.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:13.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.690][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:13.692][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:13.693][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.694][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.696][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:13.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:13.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.705][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:13.707][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:13.708][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.709][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:13.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:13.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:13.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:13.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:13.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:13.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:13.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:13.840][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2023-05-26 04:08:13.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:13.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:13.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.853][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:13.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:13.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:13.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:13.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:13.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:13.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:13.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:13.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:13.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:13.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.912][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:13.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:13.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.917][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:13.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:13.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.923][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:13.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:13.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:13.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:13.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.978][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:13.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:13.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:13.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:13.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:13.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:13.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.079][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.081][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.082][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.083][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.116][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.117][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.120][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:14.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.136][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:14.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:14.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:14.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:14.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.147][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:14.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:14.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.152][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:14.154][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:14.155][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.156][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:14.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:14.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.173][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:14.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:14.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.178][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:14.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:14.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:14.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:14.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.190][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:14.191][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:14.192][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.194][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:14.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:14.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.228][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.229][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.230][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.232][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.248][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.265][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.267][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.268][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.269][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.271][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.287][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:14.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:14.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.293][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:14.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:14.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.298][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:14.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:14.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.304][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:14.305][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:14.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.308][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.309][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:14.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:14.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.326][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.372][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.378][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.383][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.385][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.386][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.388][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.389][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.405][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.411][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.416][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.422][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.424][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.425][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.426][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.428][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.443][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:14.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.448][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:14.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:14.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.454][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:14.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:14.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.459][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:14.461][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:14.462][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.463][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.465][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:14.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:14.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.480][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.485][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.496][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.498][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.499][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.500][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.501][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:14.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:14.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:14.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:14.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:14.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:14.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.533][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:14.534][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:14.535][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.537][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:14.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:14.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.553][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.555][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.557][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.565][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:14.567][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:14.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.569][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.577][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:14.579][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:14.580][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.581][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.589][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:14.591][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:14.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.593][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.601][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.603][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.605][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.613][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.615][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.618][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.626][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.627][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.630][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.638][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.640][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.643][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.651][ef$get] Asked field names are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.652][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.654][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.655][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.663][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:14.664][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:14.666][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.667][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.683][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:14.684][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:14.686][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.687][ef$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:14.696][biodb::testThat]
biodb.INFO [2023-05-26 04:08:14.698][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-05-26 04:08:14.699][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:14.701][biodb::testThat]
biodb.DEBUG[2023-05-26 04:08:14.721][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2023-05-26 04:08:14.731][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:08:14.736][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2023-05-26 04:08:14.737][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:14.739][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2023-05-26 04:08:14.741][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:08:14.803][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:14.804][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:08:14.806][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:14.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:14.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:14.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:14.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:14.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:14.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:14.824][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.825][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.827][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.828][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:14.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.862][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:14.864][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:14.865][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.866][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.868][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:14.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:14.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.877][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:14.879][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:14.880][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.881][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.883][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:14.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.892][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:14.894][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:14.895][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.896][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:14.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:14.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.907][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.909][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.910][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.912][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:14.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.923][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.925][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.926][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.927][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.929][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:14.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.939][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:14.940][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.942][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.943][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.945][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:14.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:14.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.954][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.956][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.958][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:14.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.969][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:14.971][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:14.972][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.983][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.986][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:14.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:14.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:14.996][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:14.998][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:14.999][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.001][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.003][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:15.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:15.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.013][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:15.015][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:15.016][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.018][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.020][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:15.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:15.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:15.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:15.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.036][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:15.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:15.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:15.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:15.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:15.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:15.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:15.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:15.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:15.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:15.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:15.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:15.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:15.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:15.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:15.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:15.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:15.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:15.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:15.091][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2023-05-26 04:08:15.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-05-26 04:08:15.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-05-26 04:08:15.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-05-26 04:08:15.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-05-26 04:08:15.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-05-26 04:08:15.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-05-26 04:08:15.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:15.118][biodb::testThat]
biodb.INFO [2023-05-26 04:08:15.120][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2023-05-26 04:08:15.121][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:15.122][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:15.127][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:15.128][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:15.130][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.131][ef$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:15.133][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2023-05-26 04:08:15.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:15.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:15.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:15.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:15.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:15.186][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:15.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:15.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:15.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:15.194][function(conn, opt)] With value "squalene".
biodb.DEBUG[2023-05-26 04:08:15.211][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-05-26 04:08:15.242][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:08:15.265][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-05-26 04:08:15.267][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:15.269][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-05-26 04:08:15.312][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[2023-05-26 04:08:15.316][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:15.318][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:15.320][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:08:16.729][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:08:17.945][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:17.959][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-05-26 04:08:18.061][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-05-26 04:08:18.069][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2023-05-26 04:08:18.094][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:18.096][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:18.097][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.099][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.101][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.103][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.105][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.107][ef$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:18.110][biodb::testThat]
biodb.INFO [2023-05-26 04:08:18.112][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2023-05-26 04:08:18.113][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:18.115][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:18.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:18.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:18.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:18.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:18.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:18.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:18.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:08:18.314][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:08:18.316][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-26 04:08:18.318][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:18.320][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2023-05-26 04:08:18.343][biodb::testThat]
biodb.INFO [2023-05-26 04:08:18.344][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2023-05-26 04:08:18.346][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:18.347][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:18.394][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:18.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:18.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:18.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:18.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:18.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:18.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:18.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.429][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:18.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:18.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:18.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:18.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.441][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:18.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.447][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:18.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:18.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:18.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:18.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:18.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:18.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.493][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:18.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:18.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:18.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:18.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:18.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.517][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:18.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:18.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.523][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-05-26 04:08:18.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-05-26 04:08:18.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:18.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-05-26 04:08:18.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:18.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-05-26 04:08:18.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:18.544][biodb::testThat]
biodb.INFO [2023-05-26 04:08:18.546][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-05-26 04:08:18.547][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:18.549][biodb::testThat]
biodb.INFO [2023-05-26 04:08:18.556][biodb::testThat]
biodb.INFO [2023-05-26 04:08:18.557][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-05-26 04:08:18.559][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:18.560][biodb::testThat]
biodb.INFO [2023-05-26 04:08:18.568][biodb::testThat]
biodb.INFO [2023-05-26 04:08:18.570][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2023-05-26 04:08:18.572][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:18.573][biodb::testThat]
biodb.DEBUG[2023-05-26 04:08:18.578][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2023-05-26 04:08:19.779][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2023-05-26 04:08:22.969][biodb::testThat]
biodb.INFO [2023-05-26 04:08:22.970][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2023-05-26 04:08:22.972][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:22.973][biodb::testThat]
biodb.DEBUG[2023-05-26 04:08:24.063][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[2023-05-26 04:08:25.130][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:25.131][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:25.133][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:25.134][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:25.136][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:25.137][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:25.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:25.140][ef$get] fields variable is a list.
biodb.INFO [2023-05-26 04:08:25.143][biodb::testThat]
biodb.INFO [2023-05-26 04:08:25.144][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2023-05-26 04:08:25.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:08:25.147][biodb::testThat]
biodb.TRACE[2023-05-26 04:08:25.172][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:25.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:25.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:25.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:25.179][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:25.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:25.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:25.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:25.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:25.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:25.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:25.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:25.306][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.INFO [2023-05-26 04:08:25.311][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2023-05-26 04:08:25.331][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:25.333][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:25.369][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:08:26.600][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:08:28.782][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2023-05-26 04:08:28.788][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2023-05-26 04:08:28.794][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2023-05-26 04:08:28.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2023-05-26 04:08:28.925][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[2023-05-26 04:08:28.930][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:08:28.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-26 04:08:28.934][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:28.936][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2023-05-26 04:08:28.973][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-26 04:08:28.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-26 04:08:28.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:28.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:28.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:28.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:28.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:28.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:29.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:29.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:29.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:29.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:29.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:29.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:29.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:29.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:29.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:29.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:29.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:29.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:29.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:29.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:29.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:29.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:29.077][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[2023-05-26 04:08:29.081][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:29.083][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:29.085][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:08:30.112][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:08:31.179][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:31.188][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2023-05-26 04:08:31.203][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2023-05-26 04:08:31.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:31.212][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:31.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:31.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:31.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:31.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:31.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:31.228][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2023-05-26 04:08:31.304][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:08:31.307][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2023-05-26 04:08:31.309][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:08:31.310][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:08:31.311][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:08:31.313][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:08:31.314][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:08:31.316][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:08:31.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:31.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:31.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:31.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:31.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:31.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:31.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:31.335][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2023-05-26 04:08:31.339][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:31.340][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:31.342][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2023-05-26 04:08:32.344][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2023-05-26 04:08:33.403][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:33.412][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2023-05-26 04:08:33.427][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2023-05-26 04:08:33.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2023-05-26 04:08:33.445][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:08:33.470][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:33.472][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:08:33.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:33.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:33.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:33.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:33.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:33.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:33.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:33.491][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.493][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.494][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.503][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.518][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:33.519][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:33.520][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.522][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.524][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:33.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:33.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.533][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:33.534][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:33.536][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.537][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.539][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:33.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:33.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.549][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:33.551][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:33.552][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.553][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:33.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:33.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.564][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:33.566][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:33.567][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.568][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:33.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:33.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.580][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:33.581][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:33.583][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.584][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.586][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:33.587][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:33.589][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.590][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.592][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:33.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:33.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.601][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:33.602][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:33.604][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.605][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:33.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:33.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.616][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:33.618][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:33.619][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.620][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:33.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:33.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.632][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:33.633][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:33.635][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.636][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.638][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:33.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:33.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.647][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:33.649][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:33.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.651][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.653][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:33.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:33.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:33.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:33.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:33.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:33.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:33.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:33.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:33.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:33.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:33.725][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2023-05-26 04:08:33.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:33.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:33.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:33.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:33.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:33.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:33.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:33.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:33.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:33.764][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:08:33.769][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:33.770][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:33.773][private$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[2023-05-26 04:08:35.884][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[2023-05-26 04:08:36.922][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:36.931][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2023-05-26 04:08:36.946][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2023-05-26 04:08:36.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:36.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:36.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:36.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:36.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:36.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:36.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:36.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:36.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:36.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:36.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:36.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:36.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:36.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:36.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:36.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:36.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:37.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:37.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:37.004][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:08:37.008][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:37.010][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:37.012][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:08:38.767][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:08:39.800][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:39.811][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2023-05-26 04:08:39.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2023-05-26 04:08:39.920][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:08:39.925][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:08:39.927][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-26 04:08:39.929][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:08:39.931][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-26 04:08:39.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:39.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:39.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:39.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:39.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:39.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:39.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:39.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:39.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:39.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:39.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:39.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:39.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:39.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:39.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:39.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:39.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:39.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:39.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:39.995][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:39.996][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:39.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:40.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:40.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:40.009][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:40.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:40.012][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2023-05-26 04:08:40.014][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:08:40.016][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2023-05-26 04:08:40.018][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:08:40.020][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:08:40.021][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:08:40.023][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:08:40.025][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:08:40.026][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:08:40.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:40.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:40.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:40.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:40.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:40.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:40.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:40.066][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2023-05-26 04:08:40.069][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:40.071][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:40.073][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2023-05-26 04:08:41.224][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2023-05-26 04:08:42.316][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:42.326][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2023-05-26 04:08:42.341][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2023-05-26 04:08:42.356][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2023-05-26 04:08:42.362][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:08:42.389][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:42.390][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:08:42.393][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:42.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:42.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:42.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:42.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:42.408][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:42.409][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[2023-05-26 04:08:42.413][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.414][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.417][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.429][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:42.431][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:42.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.434][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.435][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:42.437][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:42.438][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.440][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.442][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:42.444][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:42.445][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.447][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.448][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:42.450][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:42.451][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.453][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.455][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:42.456][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:42.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.459][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.461][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:42.463][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.464][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.466][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.467][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:42.469][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:42.471][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.472][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.474][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:42.475][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:42.477][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.478][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:42.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:42.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.490][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:42.491][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:42.493][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.494][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.496][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:42.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:42.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.506][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:42.508][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:42.509][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.511][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:42.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:42.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:42.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:42.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:42.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:42.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:42.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:42.586][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2023-05-26 04:08:42.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:42.612][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:42.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:42.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:42.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:42.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:42.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:42.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:42.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:42.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:42.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:42.636][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2023-05-26 04:08:42.637][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:08:42.640][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2023-05-26 04:08:42.641][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:08:42.643][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:08:42.645][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:08:42.646][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:08:42.648][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:08:42.649][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:08:42.653][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:42.654][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:42.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:42.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:42.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:42.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:42.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:42.670][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2023-05-26 04:08:42.674][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:42.675][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:42.677][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2023-05-26 04:08:43.697][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2023-05-26 04:08:44.966][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:44.975][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2023-05-26 04:08:44.989][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2023-05-26 04:08:45.002][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2023-05-26 04:08:45.007][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:08:45.043][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:45.045][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:08:45.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:45.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:45.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:45.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:45.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:45.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:45.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:45.064][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.066][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.068][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.069][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.080][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:45.082][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:45.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.084][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.086][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:45.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:45.089][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.090][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:45.093][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:45.095][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.096][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.098][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:45.099][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:45.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.102][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.103][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:45.105][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:45.106][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.108][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.109][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:45.111][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.112][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.113][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.115][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:45.117][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:45.118][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.119][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.121][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:45.122][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:45.124][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.125][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:45.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:45.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.136][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:45.138][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:45.139][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.141][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.142][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:45.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:45.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.152][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:45.153][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:45.154][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.156][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:45.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:45.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:45.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:45.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:45.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:45.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:45.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:45.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:45.217][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2023-05-26 04:08:45.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:45.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:45.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:45.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:45.246][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:45.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:45.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:45.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:45.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:45.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:45.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:45.262][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2023-05-26 04:08:45.263][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:08:45.266][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2023-05-26 04:08:45.268][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:08:45.269][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:08:45.271][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:08:45.272][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:08:45.274][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:08:45.275][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:08:45.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:45.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:45.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:45.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:45.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:45.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:45.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:45.303][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2023-05-26 04:08:45.306][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:45.308][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:45.310][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2023-05-26 04:08:46.350][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2023-05-26 04:08:54.893][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:54.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2023-05-26 04:08:54.918][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2023-05-26 04:08:54.932][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2023-05-26 04:08:54.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:08:54.964][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:54.966][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:08:54.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:54.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:54.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:54.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:54.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:54.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:54.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:54.986][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:54.987][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:54.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:54.990][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:54.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:54.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:54.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:54.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.001][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:55.002][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:55.003][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.005][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.006][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:55.008][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:55.009][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.011][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.012][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:55.014][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:55.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.016][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.018][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:55.020][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:55.021][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.022][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.024][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:55.025][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:55.027][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.028][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.030][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:55.031][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.032][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.034][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.035][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:55.037][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:55.038][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.039][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.042][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:55.043][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:55.044][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.046][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:55.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:55.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.069][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:55.070][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:55.072][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.073][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.075][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:55.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:55.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.084][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:55.086][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:55.087][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.088][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:55.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:55.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:55.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:55.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:55.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:55.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:55.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:55.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:55.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:55.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:55.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:55.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:55.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:55.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:55.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:55.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:55.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:55.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:55.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:55.151][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2023-05-26 04:08:55.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:55.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:55.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:55.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:55.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:55.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:55.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:55.192][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:55.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:55.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:55.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:55.197][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2023-05-26 04:08:55.199][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:08:55.201][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2023-05-26 04:08:55.203][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:08:55.204][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:08:55.206][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:08:55.207][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:08:55.209][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:08:55.210][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:08:55.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:55.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:55.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:55.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:55.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:55.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:55.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:55.230][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2023-05-26 04:08:55.234][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:55.235][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:55.237][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2023-05-26 04:08:56.302][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2023-05-26 04:08:57.357][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:08:57.377][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2023-05-26 04:08:57.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2023-05-26 04:08:57.404][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2023-05-26 04:08:57.410][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:08:57.434][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:08:57.436][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:08:57.438][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:57.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:57.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:57.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:57.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:57.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:57.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:08:57.456][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.457][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.459][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.460][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.471][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:57.472][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:57.473][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.475][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.476][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:08:57.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:08:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.486][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:57.488][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:57.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.490][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:08:57.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:08:57.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.501][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:57.503][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:57.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.506][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:08:57.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:08:57.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.516][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:57.518][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:57.519][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.521][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:08:57.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:08:57.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.531][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:57.533][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:57.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.536][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.537][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:57.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:08:57.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.546][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:57.548][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:57.549][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.550][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.552][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:08:57.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:57.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.561][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:57.563][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:57.564][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.565][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:57.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:08:57.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.576][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:57.577][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:57.579][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.580][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:08:57.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:08:57.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.591][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:57.593][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:57.594][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.595][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.597][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:08:57.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:08:57.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.606][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:57.607][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:57.609][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.610][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.612][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:08:57.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:08:57.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:57.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:57.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:57.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:57.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.646][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:08:57.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:08:57.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:08:57.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:08:57.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:57.690][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2023-05-26 04:08:57.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:57.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:57.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.697][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:57.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:57.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:08:57.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:57.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:08:57.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:08:57.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:08:57.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:57.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:57.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:57.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:57.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:57.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:57.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:57.724][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2023-05-26 04:08:57.726][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:08:57.728][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2023-05-26 04:08:57.730][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:08:57.731][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:08:57.733][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:08:57.734][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:08:57.735][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:08:57.737][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:08:57.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:08:57.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:08:57.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:08:57.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:08:57.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:08:57.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:08:57.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:08:57.757][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2023-05-26 04:08:57.761][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:08:57.762][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:08:57.764][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2023-05-26 04:08:59.057][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2023-05-26 04:09:02.914][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:02.923][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2023-05-26 04:09:02.938][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2023-05-26 04:09:02.951][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2023-05-26 04:09:02.967][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:02.993][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:02.995][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:02.997][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:02.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:02.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:03.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:03.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:03.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:03.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:03.014][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.016][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.017][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.019][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.030][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:03.031][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:03.032][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.034][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.036][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:03.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:03.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.045][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:03.046][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:03.048][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.049][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.051][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:03.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:03.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.060][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:03.062][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:03.063][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.064][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:03.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:03.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.075][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:03.077][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:03.078][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.079][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:03.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:03.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.090][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:03.092][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:03.094][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.095][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.097][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:03.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:03.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.107][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:03.108][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:03.110][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.111][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.113][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:03.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:03.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.123][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:03.124][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:03.126][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.127][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:03.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:03.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.139][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:03.140][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:03.142][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.143][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:03.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:03.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.155][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:03.157][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:03.158][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.159][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.161][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:03.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:03.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.171][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:03.172][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:03.174][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.175][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.177][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:03.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:03.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:03.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:03.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:03.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:03.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:03.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:03.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:03.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:03.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:03.285][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2023-05-26 04:09:03.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:03.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:03.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:03.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:03.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:03.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:03.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:03.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:03.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:03.303][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:03.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:03.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:03.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:03.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:03.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:03.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:03.318][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2023-05-26 04:09:03.320][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:03.322][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2023-05-26 04:09:03.323][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:03.325][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:03.326][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:03.328][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:03.329][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:03.331][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:03.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:03.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:03.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:03.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:03.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:03.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:03.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:03.351][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2023-05-26 04:09:03.355][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:03.356][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:03.358][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2023-05-26 04:09:06.443][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2023-05-26 04:09:07.499][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:07.508][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2023-05-26 04:09:07.522][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2023-05-26 04:09:07.535][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2023-05-26 04:09:07.540][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:07.564][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:07.566][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:07.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:07.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:07.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:07.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:07.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:07.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:07.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:07.597][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.599][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.600][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.601][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.612][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:07.614][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:07.615][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.616][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:07.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:07.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.627][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:07.629][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:07.630][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.632][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.634][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:07.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:07.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.643][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:07.644][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:07.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.647][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:07.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:07.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.658][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:07.660][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:07.661][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.662][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:07.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:07.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.674][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:07.676][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:07.677][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.679][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.680][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:07.682][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:07.683][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.685][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.686][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:07.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:07.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.696][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:07.697][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:07.699][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.700][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:07.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:07.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.711][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:07.712][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:07.714][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.715][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:07.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:07.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.726][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:07.728][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:07.729][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.730][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.732][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:07.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:07.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.741][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:07.743][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:07.744][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.746][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.747][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:07.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:07.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:07.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:07.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:07.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:07.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.768][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:07.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:07.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:07.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:07.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:07.817][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2023-05-26 04:09:07.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:07.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:07.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:07.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:07.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:07.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:07.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:07.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:07.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:07.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:07.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:07.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:07.854][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:07.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:07.857][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:07.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:07.860][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2023-05-26 04:09:07.861][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:07.863][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2023-05-26 04:09:07.865][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:07.866][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:07.868][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:07.869][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:07.871][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:07.873][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:07.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:07.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:07.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:07.888][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:07.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:07.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:07.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:07.894][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2023-05-26 04:09:07.897][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:07.899][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:07.901][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2023-05-26 04:09:08.940][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2023-05-26 04:09:11.251][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:11.259][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2023-05-26 04:09:11.273][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2023-05-26 04:09:11.286][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2023-05-26 04:09:11.291][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:11.315][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:11.316][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:11.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:11.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:11.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:11.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:11.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:11.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:11.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:11.336][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.338][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.339][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.340][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.351][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:11.352][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:11.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.355][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.357][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:11.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:11.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.366][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:11.367][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:11.379][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.381][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:11.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:11.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.392][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:11.393][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:11.395][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.396][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.398][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:11.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:11.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.407][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:11.408][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:11.409][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.411][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.412][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:11.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:11.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.422][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:11.423][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:11.424][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.426][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.427][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:11.429][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:11.430][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.432][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.433][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:11.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:11.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.442][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:11.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:11.445][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.447][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:11.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:11.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.457][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:11.459][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:11.460][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.462][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:11.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:11.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.473][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:11.474][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:11.476][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.477][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.479][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:11.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:11.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.488][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:11.489][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:11.491][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.492][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:11.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:11.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:11.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:11.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:11.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:11.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:11.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:11.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:11.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:11.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:11.563][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2023-05-26 04:09:11.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:11.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:11.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:11.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:11.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:11.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:11.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:11.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:11.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:11.581][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:11.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:11.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:11.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:11.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:11.594][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:11.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:11.597][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2023-05-26 04:09:11.598][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:11.601][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2023-05-26 04:09:11.602][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:11.604][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:11.605][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:11.607][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:11.608][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:11.609][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:11.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:11.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:11.616][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:11.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:11.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:11.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:11.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:11.638][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2023-05-26 04:09:11.641][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:11.643][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:11.644][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2023-05-26 04:09:13.411][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2023-05-26 04:09:14.477][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:14.487][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2023-05-26 04:09:14.501][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2023-05-26 04:09:14.514][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2023-05-26 04:09:14.519][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:14.544][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:14.545][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:14.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:14.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:14.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:14.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:14.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:14.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:14.562][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.TRACE[2023-05-26 04:09:14.565][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.568][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.569][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.580][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:14.581][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:14.583][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.585][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.587][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:14.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:14.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.596][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:14.598][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:14.599][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.600][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:14.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.611][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:14.613][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:14.614][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.615][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.617][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:14.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:14.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.626][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:14.628][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:14.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.630][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:14.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.641][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:14.643][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:14.644][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.645][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.658][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:14.660][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:14.661][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.663][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.664][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:14.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:14.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.674][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:14.675][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:14.676][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.678][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:14.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:14.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.689][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:14.690][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:14.692][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.693][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:14.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:14.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.704][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:14.706][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:14.707][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.708][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.710][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:14.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:14.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.719][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:14.721][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:14.722][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.724][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.725][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:14.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:14.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:14.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:14.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:14.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:14.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:14.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:14.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:14.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:14.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:14.796][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2023-05-26 04:09:14.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:14.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:14.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:14.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:14.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:14.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:14.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:14.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:14.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:14.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:14.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:14.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:14.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:14.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:14.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:14.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:14.830][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2023-05-26 04:09:14.832][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:14.834][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2023-05-26 04:09:14.836][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:14.837][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:14.839][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:14.840][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:14.842][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:14.843][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:14.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:14.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:14.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:14.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:14.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:14.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:14.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:14.863][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2023-05-26 04:09:14.867][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:14.868][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:14.870][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2023-05-26 04:09:15.897][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2023-05-26 04:09:18.260][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:18.270][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2023-05-26 04:09:18.286][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2023-05-26 04:09:18.301][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2023-05-26 04:09:18.307][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:18.332][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:18.334][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:18.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:18.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:18.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:18.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:18.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:18.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:18.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:18.354][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.356][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.357][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.358][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.369][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:18.371][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:18.372][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.374][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.375][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:18.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:18.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.385][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:18.387][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:18.388][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.389][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.401][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:18.402][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:18.403][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.405][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:18.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.417][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:18.418][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:18.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.421][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.423][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:18.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:18.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.432][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:18.434][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:18.435][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.437][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.439][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:18.440][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:18.442][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.443][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.445][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:18.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:18.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.455][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:18.457][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:18.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.459][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:18.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:18.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.471][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:18.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:18.474][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.475][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:18.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:18.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.486][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:18.498][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:18.500][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.501][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.503][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:18.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.512][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:18.514][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:18.515][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.516][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.518][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:18.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:18.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.528][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:18.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:18.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:18.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:18.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:18.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:18.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:18.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:18.588][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2023-05-26 04:09:18.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:18.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:18.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:18.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:18.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:18.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:18.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:18.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:18.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:18.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:18.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:18.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:18.617][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:18.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:18.620][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:18.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:18.623][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2023-05-26 04:09:18.624][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:18.627][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2023-05-26 04:09:18.628][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:18.630][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:18.631][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:18.633][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:18.634][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:18.635][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:18.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:18.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:18.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:18.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:18.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:18.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:18.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:18.657][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2023-05-26 04:09:18.660][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:18.662][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:18.664][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2023-05-26 04:09:19.704][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2023-05-26 04:09:20.743][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:20.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2023-05-26 04:09:20.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2023-05-26 04:09:20.790][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2023-05-26 04:09:20.795][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:20.820][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:20.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:20.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:20.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:20.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:20.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:20.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:20.837][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:20.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:20.841][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:20.843][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:20.844][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.845][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:20.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:20.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.856][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:20.857][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:20.859][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.860][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.862][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:20.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:20.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.871][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:20.872][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:20.874][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.875][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.877][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:20.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:20.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.886][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:20.887][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:20.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.890][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:20.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:20.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.901][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:20.902][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:20.904][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.906][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:20.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:20.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.917][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:20.918][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:20.920][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.921][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.923][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:20.924][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:20.925][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.927][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.928][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:20.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:20.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.937][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:20.939][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:20.940][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.942][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:20.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:20.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.952][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:20.954][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:20.955][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.956][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:20.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:20.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.968][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:20.969][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:20.971][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.972][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.974][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:20.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:20.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:20.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:20.985][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.987][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.988][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:20.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:20.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:20.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:20.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:20.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:21.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:21.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:21.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:21.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:21.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:21.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:21.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:21.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:21.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:21.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:21.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:21.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:21.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:21.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:21.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:21.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:21.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:21.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:21.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:21.066][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2023-05-26 04:09:21.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:21.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:21.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.073][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:21.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:21.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:21.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:21.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:21.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:21.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:21.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:21.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:21.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:21.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:21.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:21.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:21.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:21.100][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2023-05-26 04:09:21.102][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:21.104][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2023-05-26 04:09:21.106][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:21.108][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:21.110][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:21.112][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:21.113][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:21.114][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:21.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:21.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:21.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:21.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:21.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:21.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:21.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:21.134][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2023-05-26 04:09:21.138][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:21.140][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:21.142][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2023-05-26 04:09:22.900][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2023-05-26 04:09:23.956][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:23.965][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2023-05-26 04:09:23.979][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2023-05-26 04:09:23.992][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2023-05-26 04:09:23.997][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:24.033][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:24.034][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:24.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:24.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:24.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:24.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:24.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:24.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:24.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:24.054][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.056][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.057][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.058][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.069][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:24.071][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:24.072][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.073][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.075][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:24.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:24.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.084][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:24.086][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:24.087][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.088][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:24.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:24.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.099][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:24.100][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:24.102][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.103][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.105][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:24.106][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:24.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.109][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.111][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:24.112][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:24.113][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.115][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.116][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:24.118][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:24.119][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.120][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.122][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:24.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:24.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.131][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:24.133][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:24.134][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.135][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:24.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:24.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.147][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:24.148][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:24.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.151][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.153][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:24.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:24.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.162][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:24.163][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:24.165][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.166][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.168][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:24.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:24.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.177][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:24.178][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:24.180][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.181][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:24.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:24.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:24.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:24.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:24.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:24.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.205][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:24.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:24.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:24.242][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2023-05-26 04:09:24.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:24.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:24.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:24.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:24.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:24.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:24.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:24.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:24.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:24.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:24.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:24.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:24.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:24.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:24.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:24.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:24.284][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2023-05-26 04:09:24.285][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:24.288][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2023-05-26 04:09:24.289][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:24.291][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:24.292][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:24.294][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:24.295][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:24.296][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:24.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:24.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:24.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:24.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:24.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:24.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:24.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:24.316][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2023-05-26 04:09:24.320][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:24.321][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:24.323][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2023-05-26 04:09:25.348][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2023-05-26 04:09:26.392][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:26.401][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2023-05-26 04:09:26.416][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2023-05-26 04:09:26.429][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2023-05-26 04:09:26.434][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:26.459][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:26.460][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:26.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:26.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:26.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:26.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:26.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:26.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:26.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:26.480][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.481][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.483][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.484][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.495][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:26.496][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:26.498][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.499][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.501][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:26.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:26.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.510][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:26.511][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:26.513][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.514][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.516][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:26.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:26.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.536][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:26.538][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:26.539][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.540][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.542][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:26.544][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:26.545][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.546][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.548][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:26.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:26.551][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.552][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.554][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:26.555][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:26.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.558][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:26.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:26.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.569][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:26.570][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:26.571][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.573][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:26.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:26.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.585][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:26.586][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:26.588][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.589][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:26.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:26.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.600][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:26.602][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:26.603][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.604][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.606][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:26.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:26.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.615][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:26.617][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:26.618][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.619][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:26.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:26.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:26.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:26.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:26.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:26.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:26.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:26.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:26.680][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2023-05-26 04:09:26.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:26.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:26.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:26.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:26.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:26.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:26.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:26.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:26.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:26.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:26.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:26.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:26.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:26.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:26.711][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:26.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:26.714][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2023-05-26 04:09:26.715][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:26.717][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2023-05-26 04:09:26.719][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:26.720][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:26.722][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:26.723][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:26.725][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:26.726][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:26.730][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:26.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:26.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:26.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:26.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:26.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:26.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:26.746][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2023-05-26 04:09:26.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:26.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:26.753][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2023-05-26 04:09:28.452][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2023-05-26 04:09:30.723][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:30.734][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2023-05-26 04:09:30.750][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2023-05-26 04:09:30.764][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2023-05-26 04:09:30.770][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:30.796][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:30.798][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:30.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:30.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:30.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:30.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:30.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:30.815][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:30.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:30.820][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:30.821][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:30.822][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.824][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:30.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:30.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.835][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:30.837][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:30.838][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.839][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.842][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:30.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:30.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.852][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:30.853][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:30.855][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.856][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.858][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:30.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:30.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.868][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:30.869][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:30.871][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.872][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:30.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:30.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.883][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:30.885][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:30.886][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.888][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:30.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.899][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:30.901][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:30.902][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.903][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.905][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:30.907][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:30.908][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.910][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.911][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:30.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:30.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.921][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:30.923][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:30.924][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.925][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.927][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:30.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:30.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.937][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:30.938][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:30.954][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.956][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:30.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:30.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.967][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:30.969][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:30.970][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.972][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.974][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:30.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:30.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:30.984][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:30.985][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.987][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.988][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:30.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:30.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:30.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:30.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:30.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:31.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:31.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:31.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:31.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:31.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:31.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:31.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:31.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:31.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:31.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:31.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:31.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:31.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:31.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:31.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:31.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:31.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:31.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:31.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:31.058][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2023-05-26 04:09:31.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:31.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.065][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:31.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:31.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:31.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:31.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:31.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:31.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:31.075][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:31.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:31.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:31.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:31.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:31.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:31.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:31.091][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2023-05-26 04:09:31.092][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:31.095][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2023-05-26 04:09:31.096][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:31.098][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:31.099][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:31.101][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:31.102][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:31.103][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:31.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:31.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:31.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:31.118][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:31.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:31.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:31.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:31.123][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2023-05-26 04:09:31.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:31.128][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:31.130][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2023-05-26 04:09:32.181][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2023-05-26 04:09:33.221][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:33.245][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2023-05-26 04:09:33.262][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2023-05-26 04:09:33.277][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2023-05-26 04:09:33.284][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:33.312][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:33.314][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:33.316][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:33.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:33.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:33.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:33.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:33.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:33.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:33.335][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.337][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.338][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.339][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.351][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:33.353][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:33.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.356][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.357][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:33.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:33.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.367][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:33.369][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:33.370][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.372][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.374][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:33.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:33.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.383][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:33.385][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:33.386][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.388][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:33.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:33.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.399][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:33.401][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:33.402][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.404][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.406][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:33.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:33.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.415][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:33.417][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:33.419][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.420][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.422][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:33.424][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:33.425][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.426][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.428][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:33.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:33.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.438][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:33.439][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:33.441][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.442][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:33.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:33.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.455][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:33.456][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:33.458][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.459][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.461][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:33.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:33.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.471][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:33.472][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:33.474][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.475][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.477][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:33.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:33.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.487][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:33.489][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:33.490][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.492][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.494][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:33.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:33.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:33.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:33.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:33.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:33.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:33.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:33.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:33.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:33.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:33.577][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2023-05-26 04:09:33.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:33.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:33.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:33.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:33.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:33.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:33.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:33.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:33.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:33.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:33.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:33.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:33.607][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:33.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:33.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:33.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:33.613][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2023-05-26 04:09:33.615][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:33.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2023-05-26 04:09:33.619][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:33.621][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:33.622][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:33.624][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:33.625][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:33.627][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:33.631][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:33.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:33.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:33.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:33.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:33.645][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:33.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:33.648][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2023-05-26 04:09:33.652][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:33.654][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:33.656][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2023-05-26 04:09:34.715][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2023-05-26 04:09:35.757][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:35.768][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2023-05-26 04:09:35.783][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2023-05-26 04:09:35.797][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2023-05-26 04:09:35.811][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:35.842][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:35.844][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:35.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:35.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:35.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:35.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:35.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:35.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:35.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:35.865][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:35.867][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:35.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.870][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:35.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:35.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.882][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:35.884][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:35.885][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.887][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.889][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:35.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:35.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.898][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:35.900][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:35.902][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.903][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.905][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:35.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:35.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.915][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:35.916][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:35.918][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.919][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.921][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:35.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:35.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.931][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:35.932][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:35.934][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.935][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:35.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:35.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.948][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:35.950][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:35.951][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.952][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.954][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:35.956][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:35.957][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.959][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.961][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:35.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:35.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.971][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:35.972][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:35.974][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.975][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:35.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:35.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.987][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:35.989][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:35.990][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.992][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:35.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:35.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:35.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:35.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.004][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:36.005][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:36.007][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.008][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.010][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:36.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:36.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.020][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:36.022][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:36.023][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.024][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.026][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:36.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:36.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:36.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:36.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:36.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:36.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:36.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:36.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:36.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:36.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:36.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:36.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:36.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:36.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:36.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:36.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:36.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:36.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:36.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:36.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:36.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:36.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:36.111][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2023-05-26 04:09:36.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:36.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:36.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:36.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:36.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:36.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:36.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:36.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:36.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:36.131][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:36.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:36.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:36.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:36.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:36.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:36.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:36.148][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2023-05-26 04:09:36.150][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:36.152][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2023-05-26 04:09:36.154][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:36.156][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:36.157][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:36.159][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:36.160][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:36.162][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:36.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:36.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:36.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:36.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:36.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:36.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:36.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:36.183][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2023-05-26 04:09:36.187][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:36.189][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:36.191][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2023-05-26 04:09:37.207][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2023-05-26 04:09:39.298][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:39.309][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2023-05-26 04:09:39.326][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2023-05-26 04:09:39.343][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2023-05-26 04:09:39.348][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:39.375][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:39.377][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:39.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:39.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:39.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:39.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:39.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:39.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:39.407][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[2023-05-26 04:09:39.412][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.414][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.417][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.429][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:39.431][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:39.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.433][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.435][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:39.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:39.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.446][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:39.447][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:39.449][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.451][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:39.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:39.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.463][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:39.465][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:39.466][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.467][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:39.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:39.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.479][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:39.481][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:39.482][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.484][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:39.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:39.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.496][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:39.498][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:39.499][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.501][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.503][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:39.504][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:39.506][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.507][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.509][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:39.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:39.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.519][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:39.521][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:39.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.524][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:39.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:39.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.536][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:39.538][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:39.539][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.541][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.543][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:39.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:39.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.553][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:39.555][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:39.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.557][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:39.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:39.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.569][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:39.571][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:39.572][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.574][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.576][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:39.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:39.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:39.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:39.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:39.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:39.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:39.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:39.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:39.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:39.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:39.653][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2023-05-26 04:09:39.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:39.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:39.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:39.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:39.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:39.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:39.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:39.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:39.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:39.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:39.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:39.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:39.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:39.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:39.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:39.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:39.699][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2023-05-26 04:09:39.701][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:39.703][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2023-05-26 04:09:39.705][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:39.707][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:39.708][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:39.710][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:39.711][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:39.713][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:39.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:39.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:39.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:39.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:39.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:39.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:39.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:39.734][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2023-05-26 04:09:39.738][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:39.740][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:39.742][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2023-05-26 04:09:40.765][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2023-05-26 04:09:41.810][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:41.819][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2023-05-26 04:09:41.834][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2023-05-26 04:09:41.848][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2023-05-26 04:09:41.854][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:41.879][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:41.881][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:41.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:41.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:41.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:41.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:41.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:41.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:41.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:41.901][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:41.902][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:41.904][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.905][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:41.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:41.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.915][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:41.917][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:41.918][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.920][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.921][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:41.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:41.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.946][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:41.947][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:41.949][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.950][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:41.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:41.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.962][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:41.963][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:41.965][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.966][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:41.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:41.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.977][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:41.979][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:41.980][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.982][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.983][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:41.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:41.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.993][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:41.994][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:41.996][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:41.997][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:41.999][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:42.000][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.002][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.003][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.005][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:42.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.015][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.016][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.017][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.019][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.030][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:42.032][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:42.033][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.034][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:42.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:42.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.045][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:42.047][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:42.048][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.050][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.052][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:42.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:42.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.061][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:42.063][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:42.064][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.066][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.067][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:42.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:42.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:42.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:42.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:42.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:42.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:42.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:42.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:42.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:42.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:42.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:42.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:42.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:42.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:42.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:42.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:42.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:42.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:42.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:42.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:42.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:42.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.137][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2023-05-26 04:09:42.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.212][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:09:42.216][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:09:42.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-26 04:09:42.220][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:09:42.222][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-26 04:09:42.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.348][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.517][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.531][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.560][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.579][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.595][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.699][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.797][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.798][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:42.850][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:42.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:42.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:42.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:42.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:42.863][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:42.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:42.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:42.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.931][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:42.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:42.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:42.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:43.018][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:09:43.023][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:43.024][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:43.027][private$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[2023-05-26 04:09:44.041][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[2023-05-26 04:09:45.089][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:45.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2023-05-26 04:09:45.113][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2023-05-26 04:09:45.122][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[2023-05-26 04:09:45.126][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:45.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:45.130][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:09:48.866][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:09:49.976][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:49.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2023-05-26 04:09:50.001][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2023-05-26 04:09:50.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:50.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:50.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:50.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:50.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:50.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:50.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:50.024][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2023-05-26 04:09:50.025][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:50.027][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2023-05-26 04:09:50.029][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:50.031][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:50.032][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:50.033][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:50.035][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:50.036][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:50.040][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:50.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:50.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:50.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:50.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:50.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:50.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:50.056][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2023-05-26 04:09:50.059][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:50.061][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:50.063][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2023-05-26 04:09:51.080][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2023-05-26 04:09:52.152][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:52.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2023-05-26 04:09:52.176][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2023-05-26 04:09:52.190][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2023-05-26 04:09:52.195][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:52.220][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:52.221][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:52.223][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:52.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:52.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:52.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:52.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:52.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:52.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:52.256][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.261][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.272][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:52.273][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:52.274][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.276][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.278][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:52.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:52.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.287][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:52.289][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:52.290][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.292][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:52.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:52.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.303][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:52.305][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:52.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.308][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:52.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:52.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.320][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:52.321][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:52.322][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.324][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.326][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:52.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:52.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:52.337][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:52.338][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.339][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.341][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:52.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:52.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.350][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:52.352][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:52.353][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.355][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.357][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:52.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:52.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.366][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.367][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.369][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.370][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.382][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:52.383][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:52.384][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.386][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:52.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.398][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:52.399][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:52.401][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.402][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.404][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:52.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:52.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.413][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:52.415][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:52.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.418][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:52.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:52.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:52.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:52.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:52.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:52.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:52.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:52.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:52.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:52.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:52.500][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2023-05-26 04:09:52.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.513][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:52.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:52.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:52.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:52.530][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:52.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:52.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:52.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:52.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:52.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:52.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:52.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:52.553][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:52.554][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:52.555][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:52.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:52.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:52.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:52.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:52.569][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2023-05-26 04:09:52.571][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:09:52.573][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2023-05-26 04:09:52.575][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:09:52.576][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:09:52.578][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:09:52.579][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:09:52.581][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:09:52.582][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:09:52.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:52.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:52.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:52.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:52.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:52.601][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:52.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:09:52.603][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2023-05-26 04:09:52.607][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:09:52.609][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:09:52.611][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2023-05-26 04:09:56.924][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2023-05-26 04:09:57.974][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:09:57.984][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2023-05-26 04:09:58.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2023-05-26 04:09:58.015][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2023-05-26 04:09:58.021][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:09:58.046][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:09:58.048][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:09:58.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.085][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.086][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.088][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.089][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.101][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:58.102][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:58.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.105][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.107][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:09:58.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:09:58.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.117][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:58.119][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:58.120][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.122][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:09:58.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:09:58.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.134][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:58.135][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:58.137][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.138][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:09:58.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:09:58.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.149][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:58.151][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:58.152][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.154][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:09:58.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:09:58.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.166][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:58.168][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:09:58.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.170][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.172][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:58.174][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:58.175][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.176][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.178][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:09:58.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:58.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.188][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.189][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.191][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.192][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.203][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:58.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:58.206][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.207][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.209][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:09:58.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:09:58.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.219][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:58.220][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:58.221][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.223][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.225][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:09:58.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:09:58.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.234][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:58.235][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:58.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.238][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.240][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:09:58.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:09:58.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:58.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:58.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.255][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:58.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:58.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:09:58.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:09:58.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:09:58.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:09:58.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.310][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2023-05-26 04:09:58.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.397][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:09:58.402][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:09:58.404][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-26 04:09:58.405][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:09:58.407][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-26 04:09:58.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.466][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.495][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.571][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.611][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.924][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.952][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:58.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:58.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:58.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:58.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:58.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:58.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:58.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:58.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:58.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:58.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:58.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.006][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.059][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.150][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:09:59.155][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:09:59.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2023-05-26 04:09:59.159][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:09:59.161][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2023-05-26 04:09:59.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.278][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.400][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.450][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.500][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.513][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.546][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.566][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.567][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.591][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.608][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.773][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.801][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:09:59.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:09:59.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.876][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-26 04:09:59.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-26 04:09:59.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:09:59.898][biodb::testThat]
biodb.INFO [2023-05-26 04:09:59.899][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-05-26 04:09:59.901][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:09:59.902][biodb::testThat]
biodb.TRACE[2023-05-26 04:09:59.906][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-26 04:09:59.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-26 04:09:59.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:59.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:59.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:59.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:59.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:59.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:59.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:09:59.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:59.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:09:59.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:09:59.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:09:59.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:09:59.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:09:59.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:09:59.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:09:59.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:09:59.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:09:59.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:00.015][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:00.019][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:00.021][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-05-26 04:10:00.023][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:00.025][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-05-26 04:10:00.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:00.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:00.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:00.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:00.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:00.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:00.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:00.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:00.061][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:00.066][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:00.068][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-05-26 04:10:00.069][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:00.071][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-05-26 04:10:00.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:00.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:00.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:00.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:00.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:00.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:00.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:00.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:00.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:00.117][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:00.121][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:00.123][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-05-26 04:10:00.125][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:00.127][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-05-26 04:10:00.130][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:10:00.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:00.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:00.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:00.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:00.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:00.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:00.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:00.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.159][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:00.161][private$selectFields]
biodb.TRACE[2023-05-26 04:10:00.162][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:00.163][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:00.164][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:00.166][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.169][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.170][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.171][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.173][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.174][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.176][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.177][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:00.178][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:00.180][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.181][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.182][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.184][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.185][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:00.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.216][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-05-26 04:10:00.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:00.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:00.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:00.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:00.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:00.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:00.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:00.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.245][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:00.246][private$selectFields]
biodb.TRACE[2023-05-26 04:10:00.247][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:00.248][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:00.250][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:00.251][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.253][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.254][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.255][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.257][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.258][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.261][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.262][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:00.263][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:00.265][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.266][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.267][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.269][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.270][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:00.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:00.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.288][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-26 04:10:00.290][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:10:00.291][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-26 04:10:00.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:00.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:00.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:00.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:00.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:00.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:00.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:00.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:00.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:00.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:00.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:00.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:00.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:00.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:00.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:00.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:00.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:00.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:00.486][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[2023-05-26 04:10:00.490][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:00.492][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:00.494][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:10:01.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:10:02.589][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:02.598][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2023-05-26 04:10:02.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2023-05-26 04:10:02.622][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:02.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:02.628][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:02.631][private$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[2023-05-26 04:10:03.681][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[2023-05-26 04:10:07.043][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:07.052][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2023-05-26 04:10:07.067][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2023-05-26 04:10:07.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:07.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:07.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:07.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:07.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:07.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:07.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:07.218][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:10:07.252][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:07.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.279][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.280][private$selectFields]
biodb.TRACE[2023-05-26 04:10:07.281][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:07.283][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:07.284][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.285][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.287][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.288][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.289][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.291][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.292][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.293][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.295][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.296][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.297][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.298][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.300][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.302][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.303][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.304][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:07.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.322][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-05-26 04:10:07.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.334][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:07.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.406][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.407][private$selectFields]
biodb.TRACE[2023-05-26 04:10:07.408][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:07.410][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:07.411][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.412][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.414][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.415][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.416][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.418][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.419][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.420][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.421][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.423][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.438][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.439][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.441][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.442][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.443][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.445][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:07.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.463][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-26 04:10:07.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.477][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.479][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[2023-05-26 04:10:07.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.492][private$selectFields]
biodb.TRACE[2023-05-26 04:10:07.494][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:07.495][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:07.496][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.498][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.499][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.501][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.502][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.506][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.509][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.510][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.511][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:07.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.514][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.516][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.517][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.518][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:07.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:07.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.537][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-05-26 04:10:07.538][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:10:07.539][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-26 04:10:07.551][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-26 04:10:07.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-26 04:10:07.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:10:07.558][biodb::testThat]
biodb.INFO [2023-05-26 04:10:07.559][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-05-26 04:10:07.560][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:07.561][biodb::testThat]
biodb.TRACE[2023-05-26 04:10:07.566][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-26 04:10:07.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-26 04:10:07.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.577][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.588][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:07.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:07.891][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[2023-05-26 04:10:07.896][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:07.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-05-26 04:10:07.899][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:07.901][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-05-26 04:10:07.904][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:07.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:07.938][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[2023-05-26 04:10:07.942][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:07.944][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-05-26 04:10:07.946][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:07.947][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-05-26 04:10:07.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:07.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:07.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:07.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:07.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:07.964][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:07.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:07.967][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:07.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:07.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:07.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:07.984][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:07.988][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:07.990][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-05-26 04:10:07.992][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:07.994][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-05-26 04:10:07.997][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:10:07.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.013][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.TRACE[2023-05-26 04:10:08.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.027][private$selectFields]
biodb.TRACE[2023-05-26 04:10:08.029][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:08.030][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:08.031][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.033][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.034][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.035][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.037][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.038][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.039][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.042][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.043][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.045][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.046][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.048][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.049][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.050][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.051][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:08.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.070][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-05-26 04:10:08.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.094][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.105][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.106][private$selectFields]
biodb.TRACE[2023-05-26 04:10:08.108][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:08.109][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:08.110][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.112][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.114][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.115][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.117][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.118][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.119][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.121][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.122][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.123][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.125][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.126][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.128][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.129][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.130][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.131][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:08.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.138][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.150][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-26 04:10:08.151][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:10:08.152][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-26 04:10:08.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:08.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.206][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:08.261][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:08.266][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:08.268][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-05-26 04:10:08.269][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:08.271][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-05-26 04:10:08.275][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:08.279][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:08.281][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-05-26 04:10:08.283][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:08.285][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-05-26 04:10:08.288][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.309][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:08.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:08.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:08.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:08.393][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:10:08.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.409][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.422][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.423][private$selectFields]
biodb.TRACE[2023-05-26 04:10:08.425][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:08.426][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:08.427][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.429][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.430][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.431][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.433][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.434][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.436][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.437][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.438][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.439][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.441][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.442][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.444][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.445][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.446][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.448][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:08.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.466][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-05-26 04:10:08.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.495][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.496][private$selectFields]
biodb.TRACE[2023-05-26 04:10:08.497][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:08.498][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:08.500][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.501][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.503][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.504][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.505][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.507][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.508][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.510][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.511][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.512][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.514][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.515][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.517][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.518][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.519][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.521][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:08.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.541][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-26 04:10:08.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.576][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.577][private$selectFields]
biodb.TRACE[2023-05-26 04:10:08.579][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:08.580][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:08.581][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.583][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.584][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.586][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.587][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.588][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.590][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.591][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.592][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.594][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.595][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.596][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.598][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.599][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.600][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.602][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:08.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.614][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.620][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-05-26 04:10:08.622][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:10:08.623][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-26 04:10:08.634][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-26 04:10:08.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-26 04:10:08.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:10:08.641][biodb::testThat]
biodb.INFO [2023-05-26 04:10:08.643][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-05-26 04:10:08.644][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:08.645][biodb::testThat]
biodb.TRACE[2023-05-26 04:10:08.649][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-05-26 04:10:08.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-05-26 04:10:08.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:08.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:08.756][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:08.760][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:08.762][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2023-05-26 04:10:08.764][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:08.766][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2023-05-26 04:10:08.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.796][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:08.802][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:08.807][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:08.808][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2023-05-26 04:10:08.817][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:08.819][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2023-05-26 04:10:08.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.833][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.849][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:08.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:08.856][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:08.860][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:08.862][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2023-05-26 04:10:08.864][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:08.865][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2023-05-26 04:10:08.868][private$bdb$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:10:08.871][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.872][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.884][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.897][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.899][private$selectFields]
biodb.TRACE[2023-05-26 04:10:08.900][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:08.901][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:08.903][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.906][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.907][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.908][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.910][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.911][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.912][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.914][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.915][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.917][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.918][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.920][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.921][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.923][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.924][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:08.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.944][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2023-05-26 04:10:08.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:08.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:08.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:08.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:08.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:08.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:08.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:08.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.972][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.973][private$selectFields]
biodb.TRACE[2023-05-26 04:10:08.975][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:08.976][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:08.977][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.979][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.980][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.981][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.983][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.984][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.985][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.987][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.988][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.989][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.991][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:08.992][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.994][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:08.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:08.996][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:08.998][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:08.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.016][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-26 04:10:09.017][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:10:09.019][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-26 04:10:09.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:09.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:09.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:09.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:09.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:09.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:09.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:09.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:09.156][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[2023-05-26 04:10:09.160][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:09.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2023-05-26 04:10:09.164][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:09.166][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2023-05-26 04:10:09.170][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[2023-05-26 04:10:09.174][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:09.176][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2023-05-26 04:10:09.177][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:09.179][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2023-05-26 04:10:09.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:09.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:09.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:09.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:09.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:09.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:09.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:09.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:09.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:09.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:09.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:09.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:09.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:09.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:09.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:09.230][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.236][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:09.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:09.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:09.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:09.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:09.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:09.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:09.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:09.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:09.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:09.280][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-05-26 04:10:09.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:09.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:09.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:09.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:09.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:09.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:09.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:09.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.316][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.317][private$selectFields]
biodb.TRACE[2023-05-26 04:10:09.319][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:09.320][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:09.321][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.323][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.324][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.325][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.327][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.328][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.329][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.331][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.333][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.334][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.336][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.337][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.339][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.340][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.341][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.343][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:09.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.361][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2023-05-26 04:10:09.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:09.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:09.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:09.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:09.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:09.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:09.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:09.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.389][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.390][private$selectFields]
biodb.TRACE[2023-05-26 04:10:09.391][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:09.392][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:09.394][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.395][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.396][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.398][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.399][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.400][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.403][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.404][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.406][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.407][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.408][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.411][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.412][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.414][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:09.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.432][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2023-05-26 04:10:09.433][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:09.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:09.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:09.444][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:09.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:09.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:09.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:09.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.460][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.461][private$selectFields]
biodb.TRACE[2023-05-26 04:10:09.462][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-05-26 04:10:09.464][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-05-26 04:10:09.465][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.466][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.468][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.469][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.471][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.472][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.473][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.475][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.476][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.477][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.479][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2023-05-26 04:10:09.480][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.481][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.483][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.484][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.485][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2023-05-26 04:10:09.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:09.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:09.504][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2023-05-26 04:10:09.505][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-05-26 04:10:09.507][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-05-26 04:10:09.538][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-05-26 04:10:09.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-05-26 04:10:09.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:09.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-05-26 04:10:09.551][biodb::testThat]
biodb.INFO [2023-05-26 04:10:09.552][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2023-05-26 04:10:09.554][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:09.555][biodb::testThat]
biodb.DEBUG[2023-05-26 04:10:09.558][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-05-26 04:10:09.559][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:10:09.561][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-05-26 04:10:09.563][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:10:09.564][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:10:09.566][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:10:09.567][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:10:09.569][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:10:09.570][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:10:09.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:09.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:09.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:09.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:09.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:09.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:09.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:09.589][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2023-05-26 04:10:09.593][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:09.595][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:09.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2023-05-26 04:10:10.603][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2023-05-26 04:10:11.614][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:11.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2023-05-26 04:10:11.637][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2023-05-26 04:10:11.651][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2023-05-26 04:10:11.656][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:10:11.678][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:10:11.679][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:10:11.681][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:11.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:11.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:11.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:11.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:11.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:11.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:11.698][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.700][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.701][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.702][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.713][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:10:11.714][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:10:11.716][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.717][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.719][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:11.720][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:11.721][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.723][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.725][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:10:11.726][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:10:11.727][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.729][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.730][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:10:11.732][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:10:11.733][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.734][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.736][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:11.738][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:11.739][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.740][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.742][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:10:11.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:11.755][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.757][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.758][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:11.760][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:11.761][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.762][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.764][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:11.766][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:11.767][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.768][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.770][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:10:11.771][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:10:11.773][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.774][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.776][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:10:11.777][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:10:11.778][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.780][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:11.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:11.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:11.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:11.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:11.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:11.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:11.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:11.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:11.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:11.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:11.841][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2023-05-26 04:10:11.842][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-05-26 04:10:11.850][biodb::testThat]
biodb.INFO [2023-05-26 04:10:11.852][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-05-26 04:10:11.853][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:11.854][biodb::testThat]
biodb.DEBUG[2023-05-26 04:10:11.868][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2023-05-26 04:10:11.869][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2023-05-26 04:10:11.870][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2023-05-26 04:10:11.873][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2023-05-26 04:10:11.874][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2023-05-26 04:10:11.876][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:10:11.877][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:10:11.879][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:10:11.880][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:10:11.881][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:10:11.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:11.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:11.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:11.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:11.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:11.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:11.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:11.902][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2023-05-26 04:10:11.906][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:11.907][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:11.909][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2023-05-26 04:10:13.676][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2023-05-26 04:10:14.797][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:14.806][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2023-05-26 04:10:14.831][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2023-05-26 04:10:14.838][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:14.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:14.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:14.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:14.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:14.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:14.852][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[2023-05-26 04:10:14.854][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2023-05-26 04:10:14.857][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:14.859][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:14.861][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2023-05-26 04:10:15.897][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2023-05-26 04:10:17.804][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:17.813][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2023-05-26 04:10:17.828][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2023-05-26 04:10:17.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:17.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:17.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:17.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:17.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:17.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:17.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:17.850][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2023-05-26 04:10:17.853][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:17.855][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:17.857][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2023-05-26 04:10:18.888][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2023-05-26 04:10:19.943][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:19.952][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2023-05-26 04:10:19.966][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2023-05-26 04:10:19.980][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2023-05-26 04:10:19.999][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:10:20.022][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2023-05-26 04:10:20.024][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2023-05-26 04:10:20.026][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:20.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:20.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:20.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:20.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:20.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:20.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:20.044][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.045][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.046][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.048][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.058][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:10:20.060][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:10:20.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.063][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.064][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:20.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:20.067][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.068][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.070][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:10:20.072][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:10:20.073][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.074][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.076][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.077][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.079][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.080][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.082][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.083][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.085][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.086][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.088][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:10:20.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:20.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.092][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.093][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.096][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.097][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.099][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:20.101][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:20.102][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.103][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.105][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:10:20.107][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:10:20.108][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.109][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.111][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:10:20.112][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:10:20.114][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.115][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:20.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:20.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:20.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:20.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:20.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:20.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:20.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:20.178][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.180][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.181][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.182][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.193][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:10:20.195][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:10:20.196][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.198][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.199][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:10:20.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:10:20.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.209][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:20.210][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:20.212][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.213][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.215][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:20.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:20.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.224][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:10:20.226][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:10:20.227][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.228][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.230][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:10:20.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:10:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.247][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.248][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.250][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.251][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.262][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.263][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.265][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.266][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.268][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.277][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:10:20.279][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:20.280][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.281][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.283][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:10:20.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:20.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.292][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.294][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.295][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.296][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.307][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:20.309][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:20.310][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.312][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:20.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:20.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.323][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:10:20.324][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:10:20.326][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.327][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.329][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:10:20.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:10:20.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.338][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:10:20.339][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:10:20.341][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.342][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.344][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:10:20.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:10:20.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.353][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.360][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:20.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:20.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:20.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:20.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:20.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:20.411][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:20.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:20.415][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.417][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.418][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.420][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.431][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:10:20.432][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:10:20.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.435][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.437][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:10:20.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:10:20.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.446][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:20.448][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:20.449][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.450][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.452][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:20.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:20.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.462][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:10:20.463][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:10:20.465][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.466][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:10:20.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:10:20.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.477][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.479][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.480][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.481][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.483][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:10:20.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.500][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.501][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.503][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.504][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.506][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:20.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.515][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:10:20.517][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:20.518][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.520][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.522][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:10:20.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:20.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.531][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.533][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.534][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.535][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:20.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.547][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:20.548][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:20.549][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.551][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:20.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:20.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.563][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:10:20.565][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:10:20.566][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.568][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.569][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:10:20.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:10:20.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.579][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:10:20.580][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:10:20.581][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.583][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.585][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:10:20.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:10:20.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:20.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.677][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:20.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:20.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:20.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:20.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:20.688][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2023-05-26 04:10:20.689][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-05-26 04:10:20.691][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-05-26 04:10:20.707][biodb::testThat]
biodb.INFO [2023-05-26 04:10:20.709][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2023-05-26 04:10:20.710][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:20.711][biodb::testThat]
biodb.INFO [2023-05-26 04:10:20.749][biodb::testThat]
biodb.INFO [2023-05-26 04:10:20.750][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2023-05-26 04:10:20.752][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:20.753][biodb::testThat]
biodb.INFO [2023-05-26 04:10:20.763][biodb::testThat]
biodb.INFO [2023-05-26 04:10:20.765][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2023-05-26 04:10:20.766][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:20.768][biodb::testThat]
biodb.DEBUG[2023-05-26 04:10:20.772][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[2023-05-26 04:10:20.776][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:20.777][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:20.780][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:10:23.639][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:10:24.979][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:24.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2023-05-26 04:10:25.003][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2023-05-26 04:10:25.026][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:25.028][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:25.029][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:25.030][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:25.032][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:25.033][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:25.034][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:25.036][ef$get] fields variable is a list.
biodb.INFO [2023-05-26 04:10:25.038][biodb::testThat]
biodb.INFO [2023-05-26 04:10:25.039][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2023-05-26 04:10:25.040][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:25.041][biodb::testThat]
biodb.ERROR[2023-05-26 04:10:25.060][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-05-26 04:10:25.082][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-05-26 04:10:25.096][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-26 04:10:25.098][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-05-26 04:10:25.099][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-05-26 04:10:25.101][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-26 04:10:25.102][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.104][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.107][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-26 04:10:25.132][biodb::testContext]
biodb.INFO [2023-05-26 04:10:25.134][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:10:25.135][biodb::testContext] Test context - Test conversions
biodb.INFO [2023-05-26 04:10:25.136][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:10:25.138][biodb::testContext]
biodb.INFO [2023-05-26 04:10:25.144][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:10:25.146][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-26 04:10:25.151][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:25.153][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-26 04:10:25.154][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-26 04:10:25.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.159][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-26 04:10:25.161][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-26 04:10:25.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.166][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-26 04:10:25.167][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-26 04:10:25.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.171][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[2023-05-26 04:10:25.173][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-26 04:10:25.174][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-26 04:10:25.175][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-26 04:10:25.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.180][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-26 04:10:25.182][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-26 04:10:25.183][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-26 04:10:25.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.188][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-26 04:10:25.190][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-26 04:10:25.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.195][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-26 04:10:25.196][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-26 04:10:25.198][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-26 04:10:25.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.203][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-26 04:10:25.204][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-26 04:10:25.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.210][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-26 04:10:25.211][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-26 04:10:25.212][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-26 04:10:25.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.217][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:10:25.219][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-26 04:10:25.220][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-26 04:10:25.222][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-26 04:10:25.223][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-26 04:10:25.224][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-26 04:10:25.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.230][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-26 04:10:25.231][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-26 04:10:25.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.236][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-26 04:10:25.238][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-26 04:10:25.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.243][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-26 04:10:25.244][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-26 04:10:25.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.249][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-26 04:10:25.251][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-26 04:10:25.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.256][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-26 04:10:25.257][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-26 04:10:25.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.262][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:10:25.264][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-26 04:10:25.268][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-26 04:10:25.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.274][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-26 04:10:25.275][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-26 04:10:25.277][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-26 04:10:25.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.282][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-26 04:10:25.285][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.286][self$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[2023-05-26 04:10:25.288][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.289][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:25.290][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.292][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.293][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.295][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.296][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:10:25.297][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:25.299][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.300][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-26 04:10:25.302][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:25.303][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.305][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.306][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:25.306][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:25.306][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:25.306][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:10:25.306][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:10:25.307][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:25.309][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.310][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.311][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:25.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.316][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.317][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.318][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:25.320][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:25.321][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.322][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.324][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-26 04:10:25.326][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.328][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:10:25.329][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.331][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:25.332][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.334][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.335][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.336][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.338][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:10:25.339][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:25.341][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.342][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-26 04:10:25.343][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:25.345][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.346][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.348][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:25.348][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:25.348][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:25.348][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:10:25.348][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:10:25.349][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:25.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.352][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.353][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:25.354][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.356][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.357][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.358][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.360][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:25.369][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:25.370][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.372][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.373][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-26 04:10:25.376][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.378][self$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[2023-05-26 04:10:25.379][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.380][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:25.382][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.383][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.385][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.386][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.388][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:10:25.389][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:25.390][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.392][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-26 04:10:25.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:25.395][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.396][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.398][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.399][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:25.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.402][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.403][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:25.404][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.407][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.409][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:25.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:25.413][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.414][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.416][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-26 04:10:25.419][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.420][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:10:25.421][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:25.424][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.426][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.427][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.429][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.430][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:10:25.432][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:25.433][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.434][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-26 04:10:25.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:25.437][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.439][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.440][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:25.443][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.446][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:25.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.451][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.452][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:25.454][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:25.455][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.456][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:25.458][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:25.460][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.475][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.501][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.513][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[2023-05-26 04:10:25.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.545][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.DEBUG[2023-05-26 04:10:25.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.551][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.DEBUG[2023-05-26 04:10:25.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.558][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[2023-05-26 04:10:25.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.572][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-26 04:10:25.574][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-26 04:10:25.576][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-26 04:10:25.578][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-26 04:10:25.580][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:10:25.582][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-26 04:10:25.584][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-26 04:10:25.586][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-26 04:10:25.588][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-26 04:10:25.590][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-26 04:10:25.592][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:10:25.594][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-26 04:10:25.596][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-26 04:10:25.598][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-26 04:10:25.600][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-26 04:10:25.610][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:10:25.612][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-26 04:10:25.614][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-26 04:10:25.616][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:10:25.618][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-26 04:10:25.620][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-26 04:10:25.622][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-26 04:10:25.624][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-26 04:10:25.626][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-26 04:10:25.628][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-26 04:10:25.630][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-26 04:10:25.632][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-26 04:10:25.634][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-26 04:10:25.636][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-26 04:10:25.638][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-26 04:10:25.640][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-26 04:10:25.643][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-26 04:10:25.645][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-26 04:10:25.647][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-26 04:10:25.649][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-26 04:10:25.651][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-26 04:10:25.653][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-26 04:10:25.655][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-26 04:10:25.657][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-26 04:10:25.659][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-26 04:10:25.661][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-26 04:10:25.663][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-26 04:10:25.665][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-26 04:10:25.667][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-26 04:10:25.669][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-26 04:10:25.671][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-26 04:10:25.673][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-26 04:10:25.675][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-26 04:10:25.678][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-26 04:10:25.680][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-26 04:10:25.682][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-26 04:10:25.684][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-26 04:10:25.686][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-26 04:10:25.688][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-26 04:10:25.690][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-26 04:10:25.692][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-26 04:10:25.694][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-26 04:10:25.696][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-26 04:10:25.698][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-26 04:10:25.700][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-26 04:10:25.703][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-26 04:10:25.705][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-26 04:10:25.707][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-26 04:10:25.709][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-26 04:10:25.711][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-26 04:10:25.713][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-26 04:10:25.715][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:10:25.717][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:10:25.719][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-26 04:10:25.721][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-26 04:10:25.723][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-26 04:10:25.725][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-26 04:10:25.727][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-26 04:10:25.729][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-26 04:10:25.731][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-26 04:10:25.733][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-26 04:10:25.735][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-26 04:10:25.737][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-26 04:10:25.739][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-26 04:10:25.741][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-26 04:10:25.743][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-26 04:10:25.745][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-26 04:10:25.747][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-26 04:10:25.749][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-26 04:10:25.751][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:10:25.753][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:25.754][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.757][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.767][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[2023-05-26 04:10:25.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.786][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.794][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[2023-05-26 04:10:25.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.822][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[2023-05-26 04:10:25.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.831][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[2023-05-26 04:10:25.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.899][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[2023-05-26 04:10:25.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:25.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.918][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[2023-05-26 04:10:25.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:25.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:25.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:25.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:25.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:25.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:25.928][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[2023-05-26 04:10:25.930][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-05-26 04:10:25.932][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-05-26 04:10:25.936][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.937][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.939][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.941][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:25.942][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.944][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.945][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.947][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-05-26 04:10:25.948][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-26 04:10:25.950][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:25.952][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.953][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-05-26 04:10:25.955][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-05-26 04:10:25.956][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-05-26 04:10:25.958][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:25.959][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:25.959][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:25.959][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:25.961][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-26 04:10:25.962][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.965][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:25.967][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:25.968][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:25.970][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:25.971][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:10:25.971][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-05-26 04:10:25.973][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:25.974][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:25.976][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:25.977][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-05-26 04:10:25.977][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-05-26 04:10:25.980][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:10:25.982][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:10:25.985][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-05-26 04:10:25.987][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:10:25.989][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:10:25.992][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:10:25.997][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-05-26 04:10:25.999][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-05-26 04:10:26.001][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-05-26 04:10:26.003][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-05-26 04:10:26.005][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-26 04:10:26.006][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-26 04:10:26.008][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-05-26 04:10:26.010][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-05-26 04:10:26.012][biodb::testThat]
biodb.INFO [2023-05-26 04:10:26.013][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2023-05-26 04:10:26.015][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:26.016][biodb::testThat]
biodb.DEBUG[2023-05-26 04:10:26.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-05-26 04:10:26.028][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:26.030][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:26.031][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2023-05-26 04:10:27.050][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2023-05-26 04:10:28.570][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:28.596][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2023-05-26 04:10:28.611][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2023-05-26 04:10:28.620][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[2023-05-26 04:10:28.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:28.626][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:28.628][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:10:29.645][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:10:30.665][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:30.674][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2023-05-26 04:10:30.690][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2023-05-26 04:10:30.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:30.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:30.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:30.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:30.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:30.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:30.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:30.713][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:30.717][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:30.719][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:30.721][private$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[2023-05-26 04:10:31.724][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[2023-05-26 04:10:32.775][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:32.785][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2023-05-26 04:10:32.800][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2023-05-26 04:10:32.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:32.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:32.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:32.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:32.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:32.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:32.835][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[2023-05-26 04:10:32.857][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:32.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:32.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:32.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:32.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:32.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:32.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:32.876][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[2023-05-26 04:10:32.880][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:32.882][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-05-26 04:10:32.884][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:32.886][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-05-26 04:10:32.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:32.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:32.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:32.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:32.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:32.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:32.902][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[2023-05-26 04:10:32.904][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[2023-05-26 04:10:32.908][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:32.910][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-05-26 04:10:32.912][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:32.913][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-05-26 04:10:32.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:32.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:32.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:32.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:32.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:32.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:32.929][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[2023-05-26 04:10:32.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:32.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:32.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:32.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:32.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:32.943][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:32.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:32.949][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[2023-05-26 04:10:32.953][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:32.955][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2023-05-26 04:10:32.957][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:32.958][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2023-05-26 04:10:32.961][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:32.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:32.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:32.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:32.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:32.973][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:32.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:32.977][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[2023-05-26 04:10:32.982][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:32.984][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2023-05-26 04:10:32.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:32.987][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2023-05-26 04:10:32.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:32.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:32.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:33.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:33.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:33.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:33.004][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[2023-05-26 04:10:33.006][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[2023-05-26 04:10:33.010][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:33.012][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:33.015][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:10:34.123][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:10:35.873][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:35.883][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2023-05-26 04:10:35.898][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2023-05-26 04:10:35.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:35.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:35.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:35.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:35.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:35.917][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:35.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-26 04:10:35.923][biodb::testThat]
biodb.INFO [2023-05-26 04:10:35.925][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2023-05-26 04:10:35.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:35.928][biodb::testThat]
biodb.DEBUG[2023-05-26 04:10:35.932][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:35.937][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:35.938][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:35.941][private$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[2023-05-26 04:10:36.969][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[2023-05-26 04:10:38.245][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:38.254][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2023-05-26 04:10:38.269][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2023-05-26 04:10:38.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:38.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:38.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:38.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:38.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:38.289][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:38.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:38.295][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[2023-05-26 04:10:38.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:38.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:38.303][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2023-05-26 04:10:39.388][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2023-05-26 04:10:40.418][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:40.427][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2023-05-26 04:10:40.442][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2023-05-26 04:10:40.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:40.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:40.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:40.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-26 04:10:40.465][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-26 04:10:40.467][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-05-26 04:10:40.468][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-05-26 04:10:40.469][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-26 04:10:40.470][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:40.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:40.473][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.475][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-05-26 04:10:40.482][biodb::testContext]
biodb.INFO [2023-05-26 04:10:40.483][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:10:40.484][biodb::testContext] Test context - Test web services
biodb.INFO [2023-05-26 04:10:40.486][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:10:40.487][biodb::testContext]
biodb.INFO [2023-05-26 04:10:40.493][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:10:40.495][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-26 04:10:40.500][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:40.501][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-26 04:10:40.503][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-26 04:10:40.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.507][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[2023-05-26 04:10:40.508][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-26 04:10:40.509][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-26 04:10:40.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.515][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-26 04:10:40.516][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-26 04:10:40.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.521][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-26 04:10:40.522][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-26 04:10:40.524][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-26 04:10:40.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.529][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-26 04:10:40.530][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-26 04:10:40.532][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-26 04:10:40.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.537][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-26 04:10:40.538][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-26 04:10:40.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.544][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-26 04:10:40.545][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-26 04:10:40.546][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-26 04:10:40.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.550][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[2023-05-26 04:10:40.551][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-26 04:10:40.553][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-26 04:10:40.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.558][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-26 04:10:40.559][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-26 04:10:40.561][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-26 04:10:40.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.566][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:10:40.567][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-26 04:10:40.569][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-26 04:10:40.570][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-26 04:10:40.571][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-26 04:10:40.573][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-26 04:10:40.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.579][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-26 04:10:40.581][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-26 04:10:40.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.586][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-26 04:10:40.587][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-26 04:10:40.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.592][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-26 04:10:40.594][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-26 04:10:40.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.599][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-26 04:10:40.600][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-26 04:10:40.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.606][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-26 04:10:40.607][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-26 04:10:40.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.612][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:10:40.623][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-26 04:10:40.628][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-26 04:10:40.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.633][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-26 04:10:40.635][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-26 04:10:40.636][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-26 04:10:40.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.640][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[2023-05-26 04:10:40.642][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-26 04:10:40.644][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.645][self$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[2023-05-26 04:10:40.647][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:40.650][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.651][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.652][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.654][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.655][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:10:40.657][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:40.658][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.659][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-26 04:10:40.661][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:40.662][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.663][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.665][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:40.665][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:40.665][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:40.665][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:10:40.665][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:10:40.666][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:40.668][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:40.669][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:40.670][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:40.672][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:40.673][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:40.674][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.676][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.677][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:40.678][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:40.679][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.681][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.682][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-26 04:10:40.685][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.686][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:10:40.688][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.689][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:40.691][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.692][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.693][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.696][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:10:40.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:40.699][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.700][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-26 04:10:40.702][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:40.703][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.704][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.706][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:40.706][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:40.706][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:40.706][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:10:40.706][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:10:40.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:40.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:40.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:40.711][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:40.712][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:40.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:40.715][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.716][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.718][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:40.719][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:40.720][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.722][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.723][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-26 04:10:40.726][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.727][self$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[2023-05-26 04:10:40.729][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.730][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:40.731][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.733][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.734][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.735][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.737][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:10:40.738][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:40.740][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.741][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-26 04:10:40.742][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:40.744][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.745][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.747][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.748][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:40.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:40.751][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:40.752][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:40.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:40.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:40.756][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.757][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.759][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:40.760][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:40.761][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.763][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.764][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-26 04:10:40.767][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.768][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:10:40.770][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.771][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:40.772][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.774][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.776][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.777][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.779][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:10:40.780][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:40.782][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.783][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-26 04:10:40.785][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:40.786][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.788][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:40.789][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.791][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:40.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:40.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:40.794][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:40.796][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:40.797][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:40.798][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:40.800][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.801][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:40.802][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:40.804][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:40.805][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:40.807][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:40.808][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.822][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[2023-05-26 04:10:40.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.835][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[2023-05-26 04:10:40.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.841][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[2023-05-26 04:10:40.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.847][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[2023-05-26 04:10:40.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.861][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[2023-05-26 04:10:40.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.874][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[2023-05-26 04:10:40.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.881][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[2023-05-26 04:10:40.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.887][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[2023-05-26 04:10:40.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.893][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[2023-05-26 04:10:40.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.897][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.918][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[2023-05-26 04:10:40.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:40.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:40.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:40.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:40.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:40.926][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-26 04:10:40.928][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-26 04:10:40.930][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-26 04:10:40.932][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-26 04:10:40.934][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:10:40.936][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-26 04:10:40.938][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-26 04:10:40.940][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-26 04:10:40.942][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-26 04:10:40.944][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-26 04:10:40.946][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:10:40.948][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-26 04:10:40.949][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-26 04:10:40.951][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-26 04:10:40.953][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-26 04:10:40.955][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:10:40.957][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-26 04:10:40.959][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-26 04:10:40.961][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:10:40.963][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-26 04:10:40.965][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-26 04:10:40.967][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-26 04:10:40.969][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-26 04:10:40.972][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-26 04:10:40.974][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-26 04:10:40.976][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-26 04:10:40.978][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-26 04:10:40.981][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-26 04:10:40.983][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-26 04:10:40.985][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-26 04:10:40.987][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-26 04:10:40.989][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-26 04:10:40.991][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-26 04:10:40.993][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-26 04:10:40.995][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-26 04:10:40.997][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-26 04:10:41.000][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-26 04:10:41.002][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-26 04:10:41.004][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-26 04:10:41.006][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-26 04:10:41.008][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-26 04:10:41.010][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-26 04:10:41.012][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-26 04:10:41.014][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-26 04:10:41.016][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-26 04:10:41.018][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-26 04:10:41.021][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-26 04:10:41.023][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-26 04:10:41.025][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-26 04:10:41.027][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-26 04:10:41.029][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-26 04:10:41.031][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-26 04:10:41.033][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-26 04:10:41.035][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-26 04:10:41.037][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-26 04:10:41.039][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-26 04:10:41.041][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-26 04:10:41.043][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-26 04:10:41.045][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-26 04:10:41.047][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-26 04:10:41.049][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-26 04:10:41.051][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-26 04:10:41.053][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-26 04:10:41.055][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-26 04:10:41.057][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-26 04:10:41.059][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-26 04:10:41.061][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:10:41.063][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:10:41.065][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-26 04:10:41.068][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-26 04:10:41.070][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-26 04:10:41.072][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-26 04:10:41.074][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-26 04:10:41.076][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-26 04:10:41.078][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-26 04:10:41.080][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-26 04:10:41.082][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-26 04:10:41.084][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-26 04:10:41.086][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-26 04:10:41.088][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-26 04:10:41.098][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-26 04:10:41.100][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-26 04:10:41.102][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-26 04:10:41.104][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-26 04:10:41.106][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:10:41.108][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:41.109][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.111][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.113][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[2023-05-26 04:10:41.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.147][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[2023-05-26 04:10:41.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.189][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.200][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[2023-05-26 04:10:41.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.217][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[2023-05-26 04:10:41.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.244][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[2023-05-26 04:10:41.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:41.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:41.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:41.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:41.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:41.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:41.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:41.262][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[2023-05-26 04:10:41.264][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-05-26 04:10:41.266][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-05-26 04:10:41.268][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:41.270][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-26 04:10:41.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:41.272][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:41.274][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:41.275][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:41.277][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:41.278][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-05-26 04:10:41.279][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-26 04:10:41.281][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:41.282][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:41.284][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-05-26 04:10:41.285][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-05-26 04:10:41.287][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-05-26 04:10:41.288][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:41.290][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:41.290][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:41.290][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:41.291][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-26 04:10:41.293][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:41.294][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:41.296][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:41.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:41.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:41.300][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:41.301][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:10:41.301][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-05-26 04:10:41.303][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:41.304][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:41.305][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:41.307][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-05-26 04:10:41.307][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-05-26 04:10:41.309][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:10:41.311][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:10:41.313][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-05-26 04:10:41.315][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:10:41.317][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:10:41.319][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:10:41.332][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-05-26 04:10:41.334][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-05-26 04:10:41.335][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-05-26 04:10:41.337][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-05-26 04:10:41.339][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-26 04:10:41.340][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-26 04:10:41.342][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-05-26 04:10:41.344][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-05-26 04:10:41.345][biodb::testThat]
biodb.INFO [2023-05-26 04:10:41.347][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2023-05-26 04:10:41.348][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:41.349][biodb::testThat]
biodb.DEBUG[2023-05-26 04:10:41.354][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-05-26 04:10:41.358][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:41.360][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-05-26 04:10:41.362][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:41.364][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-05-26 04:10:41.368][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2023-05-26 04:10:41.373][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:41.374][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:41.376][private$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[2023-05-26 04:10:42.395][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[2023-05-26 04:10:43.420][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:43.430][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2023-05-26 04:10:43.445][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2023-05-26 04:10:43.454][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-26 04:10:43.456][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-05-26 04:10:43.458][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-05-26 04:10:43.459][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-26 04:10:43.460][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:43.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:43.462][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.465][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.466][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.INFO [2023-05-26 04:10:43.471][biodb::testContext]
biodb.INFO [2023-05-26 04:10:43.472][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:10:43.474][biodb::testContext] Test context - Non regression tests
biodb.INFO [2023-05-26 04:10:43.475][biodb::testContext] ********************************************************************************
biodb.INFO [2023-05-26 04:10:43.476][biodb::testContext]
biodb.INFO [2023-05-26 04:10:43.482][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:10:43.485][self$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-05-26 04:10:43.489][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:43.491][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-05-26 04:10:43.492][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-05-26 04:10:43.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.497][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-05-26 04:10:43.499][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-05-26 04:10:43.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.504][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-05-26 04:10:43.506][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-05-26 04:10:43.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.511][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-05-26 04:10:43.512][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-05-26 04:10:43.514][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-05-26 04:10:43.515][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.519][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-05-26 04:10:43.521][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-05-26 04:10:43.522][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-05-26 04:10:43.524][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.528][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-05-26 04:10:43.529][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-05-26 04:10:43.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.533][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[2023-05-26 04:10:43.534][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-05-26 04:10:43.536][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-05-26 04:10:43.537][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-05-26 04:10:43.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.543][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-05-26 04:10:43.544][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-05-26 04:10:43.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.549][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-05-26 04:10:43.551][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-05-26 04:10:43.563][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-05-26 04:10:43.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.569][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:10:43.570][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-05-26 04:10:43.572][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-05-26 04:10:43.573][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-05-26 04:10:43.575][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-05-26 04:10:43.576][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-05-26 04:10:43.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.581][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-05-26 04:10:43.583][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-05-26 04:10:43.584][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.588][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-05-26 04:10:43.589][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-05-26 04:10:43.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.594][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-05-26 04:10:43.596][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-05-26 04:10:43.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.601][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-05-26 04:10:43.602][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-05-26 04:10:43.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.607][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-05-26 04:10:43.609][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-05-26 04:10:43.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.614][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-05-26 04:10:43.615][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-05-26 04:10:43.620][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-05-26 04:10:43.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.625][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-05-26 04:10:43.626][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-05-26 04:10:43.628][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-05-26 04:10:43.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.633][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-05-26 04:10:43.636][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.637][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-05-26 04:10:43.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:43.642][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.643][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.644][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.647][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:10:43.649][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:43.650][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.651][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-05-26 04:10:43.653][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:43.654][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.656][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.657][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:43.657][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:43.657][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:43.657][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:10:43.657][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:10:43.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:43.660][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:43.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:43.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:43.664][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:43.665][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:43.666][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.668][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.669][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:43.670][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:43.672][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.673][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.675][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-05-26 04:10:43.677][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.679][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:10:43.680][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.681][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:43.683][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.684][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.686][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.687][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.688][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:10:43.690][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:43.691][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.693][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-05-26 04:10:43.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:43.695][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.697][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.698][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:43.698][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:43.698][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:43.698][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-05-26 04:10:43.698][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-05-26 04:10:43.700][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:43.701][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:43.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:43.704][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:43.705][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:43.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:43.707][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.709][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.710][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:43.711][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:43.713][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.714][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.716][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-05-26 04:10:43.718][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.720][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-05-26 04:10:43.721][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.722][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:43.724][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.725][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.727][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.730][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-05-26 04:10:43.731][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:43.732][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.734][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-05-26 04:10:43.735][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:43.736][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.738][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.739][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.741][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:43.742][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:43.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:43.745][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:43.746][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:43.747][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:43.749][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.750][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.751][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:43.753][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:43.754][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.755][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.757][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-05-26 04:10:43.760][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.761][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-05-26 04:10:43.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.764][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:43.765][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.766][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.768][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.769][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.771][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-05-26 04:10:43.772][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:43.774][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.775][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-05-26 04:10:43.776][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:43.778][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.779][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:43.781][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.782][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-05-26 04:10:43.783][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:43.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:43.786][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:43.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:43.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:43.797][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:43.799][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.801][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:43.802][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:43.803][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:43.805][self$setPropertyValue]
biodb.DEBUG[2023-05-26 04:10:43.806][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:43.808][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.822][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[2023-05-26 04:10:43.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.835][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[2023-05-26 04:10:43.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.841][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[2023-05-26 04:10:43.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.847][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[2023-05-26 04:10:43.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.866][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.DEBUG[2023-05-26 04:10:43.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.891][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[2023-05-26 04:10:43.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.897][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[2023-05-26 04:10:43.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:43.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:43.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:43.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:43.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:43.916][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[2023-05-26 04:10:43.917][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-05-26 04:10:43.919][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-05-26 04:10:43.921][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-05-26 04:10:43.923][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-05-26 04:10:43.925][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:10:43.927][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-05-26 04:10:43.929][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-05-26 04:10:43.931][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-05-26 04:10:43.933][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-05-26 04:10:43.935][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-05-26 04:10:43.937][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:10:43.939][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-05-26 04:10:43.940][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-05-26 04:10:43.942][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-05-26 04:10:43.944][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-05-26 04:10:43.946][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-05-26 04:10:43.948][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-05-26 04:10:43.950][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-05-26 04:10:43.952][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:10:43.954][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-05-26 04:10:43.956][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-05-26 04:10:43.958][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-05-26 04:10:43.960][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-05-26 04:10:43.962][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-05-26 04:10:43.964][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-05-26 04:10:43.966][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-05-26 04:10:43.968][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-05-26 04:10:43.970][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-05-26 04:10:43.972][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-05-26 04:10:43.974][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-05-26 04:10:43.976][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-05-26 04:10:43.978][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-05-26 04:10:43.980][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-05-26 04:10:43.982][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-05-26 04:10:43.984][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-05-26 04:10:43.986][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-05-26 04:10:43.988][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-05-26 04:10:43.990][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-05-26 04:10:43.992][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-05-26 04:10:43.994][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-05-26 04:10:43.996][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-05-26 04:10:43.998][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-05-26 04:10:44.000][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-05-26 04:10:44.002][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-05-26 04:10:44.004][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-05-26 04:10:44.006][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-05-26 04:10:44.008][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-05-26 04:10:44.010][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-05-26 04:10:44.012][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-05-26 04:10:44.014][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-05-26 04:10:44.023][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-05-26 04:10:44.026][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-05-26 04:10:44.028][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-05-26 04:10:44.030][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-05-26 04:10:44.032][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-05-26 04:10:44.034][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-05-26 04:10:44.036][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-05-26 04:10:44.038][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-05-26 04:10:44.040][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-05-26 04:10:44.042][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-05-26 04:10:44.044][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-05-26 04:10:44.046][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-05-26 04:10:44.048][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-05-26 04:10:44.049][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-05-26 04:10:44.051][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-05-26 04:10:44.053][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-05-26 04:10:44.055][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:10:44.057][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:10:44.059][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-05-26 04:10:44.061][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-05-26 04:10:44.063][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-05-26 04:10:44.065][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-05-26 04:10:44.067][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-05-26 04:10:44.069][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-05-26 04:10:44.071][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-05-26 04:10:44.073][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-05-26 04:10:44.075][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-05-26 04:10:44.077][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-05-26 04:10:44.078][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-05-26 04:10:44.080][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-05-26 04:10:44.082][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-05-26 04:10:44.084][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-05-26 04:10:44.086][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-05-26 04:10:44.088][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-05-26 04:10:44.090][initialize] This is biodb version 1.9.0.
biodb.DEBUG[2023-05-26 04:10:44.092][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-05-26 04:10:44.093][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.095][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.105][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[2023-05-26 04:10:44.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.113][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[2023-05-26 04:10:44.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.147][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[2023-05-26 04:10:44.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.234][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[2023-05-26 04:10:44.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-05-26 04:10:44.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.252][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[2023-05-26 04:10:44.254][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/R/R-4.3.0/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2023-05-26 04:10:44.256][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2023-05-26 04:10:44.259][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:44.260][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-05-26 04:10:44.261][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:44.263][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-05-26 04:10:44.264][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:44.265][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-05-26 04:10:44.267][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:44.268][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2023-05-26 04:10:44.270][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2023-05-26 04:10:44.271][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-05-26 04:10:44.272][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:44.274][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2023-05-26 04:10:44.275][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2023-05-26 04:10:44.277][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2023-05-26 04:10:44.278][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-05-26 04:10:44.279][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-05-26 04:10:44.279][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-05-26 04:10:44.279][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-05-26 04:10:44.281][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2023-05-26 04:10:44.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:44.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:44.285][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-05-26 04:10:44.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-05-26 04:10:44.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-05-26 04:10:44.289][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-05-26 04:10:44.290][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:10:44.290][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2023-05-26 04:10:44.291][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-05-26 04:10:44.293][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-05-26 04:10:44.294][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-05-26 04:10:44.295][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2023-05-26 04:10:44.295][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2023-05-26 04:10:44.297][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-05-26 04:10:44.299][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-05-26 04:10:44.301][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2023-05-26 04:10:44.303][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-05-26 04:10:44.305][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-05-26 04:10:44.308][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-05-26 04:10:44.312][super$initialize] Initialize connector chebi.
biodb.DEBUG[2023-05-26 04:10:44.313][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2023-05-26 04:10:44.315][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2023-05-26 04:10:44.317][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2023-05-26 04:10:44.319][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-26 04:10:44.320][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2023-05-26 04:10:44.322][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2023-05-26 04:10:44.323][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2023-05-26 04:10:44.325][biodb::testThat]
biodb.INFO [2023-05-26 04:10:44.327][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2023-05-26 04:10:44.328][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-05-26 04:10:44.329][biodb::testThat]
biodb.DEBUG[2023-05-26 04:10:44.334][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2023-05-26 04:10:44.338][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:44.340][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2023-05-26 04:10:44.342][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:44.343][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2023-05-26 04:10:44.348][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[2023-05-26 04:10:44.352][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-05-26 04:10:44.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2023-05-26 04:10:44.355][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-05-26 04:10:44.357][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2023-05-26 04:10:44.361][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2023-05-26 04:10:44.363][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2023-05-26 04:10:44.365][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2023-05-26 04:10:44.367][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-05-26 04:10:44.368][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-05-26 04:10:44.370][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2023-05-26 04:10:44.371][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2023-05-26 04:10:44.373][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-05-26 04:10:44.374][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-05-26 04:10:44.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:44.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:44.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:44.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:44.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:44.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:44.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-05-26 04:10:44.393][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2023-05-26 04:10:44.397][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-05-26 04:10:44.398][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-05-26 04:10:44.400][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2023-05-26 04:10:46.446][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2023-05-26 04:10:49.283][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-05-26 04:10:49.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2023-05-26 04:10:49.319][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2023-05-26 04:10:49.333][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2023-05-26 04:10:49.338][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-05-26 04:10:49.361][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2023-05-26 04:10:49.362][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2023-05-26 04:10:49.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-05-26 04:10:49.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:49.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:49.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:49.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:49.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:49.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-05-26 04:10:49.382][ef$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.384][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.385][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.387][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.398][ef$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:10:49.399][ef$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:10:49.401][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.402][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.404][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2023-05-26 04:10:49.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2023-05-26 04:10:49.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.413][ef$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:49.415][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:49.416][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.417][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-05-26 04:10:49.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-05-26 04:10:49.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.429][ef$get] Asked field names are: inchi.
biodb.TRACE[2023-05-26 04:10:49.430][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2023-05-26 04:10:49.432][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.433][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.435][ef$get] Asked field names are: inchikey.
biodb.TRACE[2023-05-26 04:10:49.436][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2023-05-26 04:10:49.438][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.439][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.441][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:49.442][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:49.444][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.445][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.447][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:49.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-05-26 04:10:49.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.456][ef$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:10:49.458][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:49.459][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.461][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.463][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2023-05-26 04:10:49.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-05-26 04:10:49.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.472][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:49.473][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:49.475][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.476][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:49.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-05-26 04:10:49.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.488][ef$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:49.489][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:49.490][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.492][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-05-26 04:10:49.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-05-26 04:10:49.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.504][ef$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:10:49.505][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:10:49.507][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.508][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2023-05-26 04:10:49.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2023-05-26 04:10:49.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.519][ef$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:10:49.521][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:10:49.522][ef$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.524][ef$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.526][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2023-05-26 04:10:49.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2023-05-26 04:10:49.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:49.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:49.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:49.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:49.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-05-26 04:10:49.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-05-26 04:10:49.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-05-26 04:10:49.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-05-26 04:10:49.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-05-26 04:10:49.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-05-26 04:10:49.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-05-26 04:10:49.604][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2023-05-26 04:10:49.606][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-05-26 04:10:49.608][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2023-05-26 04:10:49.609][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2023-05-26 04:10:49.611][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-05-26 04:10:49.612][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-05-26 04:10:49.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-05-26 04:10:49.614][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-05-26 04:10:49.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-05-26 04:10:49.617][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-05-26 04:10:49.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 365 ]
> 
> proc.time()
   user  system elapsed 
 28.865   0.884 159.900

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn1.3810.0443.415
ChebiEntry0.2660.0040.274